Running shellcheck on nf-core/modules

shellcheck_output.md

ShellCheck results for .\modules\nf-core\abacas\main.nf:

In .\modules\nf-core\abacas\main.nf line 26:

    -r $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -r "$fasta" \

In .\modules\nf-core\abacas\main.nf line 27:

    -q $scaffold \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -q "$scaffold" \

In .\modules\nf-core\abacas\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\abacas\main.nf line 29:

    -o ${prefix}.abacas
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".abacas

In .\modules\nf-core\abacas\main.nf line 31:

mv nucmer.delta ${prefix}.abacas.nucmer.delta
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv nucmer.delta "${prefix}".abacas.nucmer.delta

In .\modules\nf-core\abacas\main.nf line 32:

mv nucmer.filtered.delta ${prefix}.abacas.nucmer.filtered.delta
                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv nucmer.filtered.delta "${prefix}".abacas.nucmer.filtered.delta

In .\modules\nf-core\abacas\main.nf line 33:

mv nucmer.tiling ${prefix}.abacas.nucmer.tiling
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv nucmer.tiling "${prefix}".abacas.nucmer.tiling

In .\modules\nf-core\abacas\main.nf line 34:

mv unused_contigs.out ${prefix}.abacas.unused.contigs.out
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv unused_contigs.out "${prefix}".abacas.unused.contigs.out

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\abricate\run\main.nf:

In .\modules\nf-core\abricate\run\main.nf line 27:

    $assembly \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$assembly" \

In .\modules\nf-core\abricate\run\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\abricate\run\main.nf line 29:

    $datadir \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$datadir" \

In .\modules\nf-core\abricate\run\main.nf line 30:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\abricate\run\main.nf line 31:

    > ${prefix}.txt
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\abricate\summary\main.nf:

In .\modules\nf-core\abricate\summary\main.nf line 26:

    $reports > ${prefix}.txt
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reports" > "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\abritamr\run\main.nf:

In .\modules\nf-core\abritamr\run\main.nf line 31:

    gzip -c -d ${fasta} > ${fasta_name}
               ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "${fasta}" > "${fasta_name}"

In .\modules\nf-core\abritamr\run\main.nf line 35:

    --contigs ${fasta_name} \
              ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --contigs "${fasta_name}" \

In .\modules\nf-core\abritamr\run\main.nf line 36:

    --prefix ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --prefix "${prefix}" \

In .\modules\nf-core\abritamr\run\main.nf line 37:

    --jobs ${task.cpus} \
           ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --jobs "${task.cpus}" \

In .\modules\nf-core\abritamr\run\main.nf line 38:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

In .\modules\nf-core\abritamr\run\main.nf line 41:

mv ${prefix}/summary_matches.txt ${prefix}.summary_matches.txt
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${prefix}"/summary_matches.txt "${prefix}".summary_matches.txt

In .\modules\nf-core\abritamr\run\main.nf line 42:

mv ${prefix}/summary_partials.txt ${prefix}.summary_partials.txt
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${prefix}"/summary_partials.txt "${prefix}".summary_partials.txt

In .\modules\nf-core\abritamr\run\main.nf line 43:

mv ${prefix}/summary_virulence.txt ${prefix}.summary_virulence.txt
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${prefix}"/summary_virulence.txt "${prefix}".summary_virulence.txt

In .\modules\nf-core\abritamr\run\main.nf line 44:

mv ${prefix}/amrfinder.out ${prefix}.amrfinder.out
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${prefix}"/amrfinder.out "${prefix}".amrfinder.out

In .\modules\nf-core\abritamr\run\main.nf line 47:

    mv ${prefix}/abritamr.txt ${prefix}.abritamr.txt
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    mv "${prefix}"/abritamr.txt "${prefix}".abritamr.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\adapterremoval\main.nf:

In .\modules\nf-core\adapterremoval\main.nf line 35:

    --file1 $reads \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --file1 "$reads" \

In .\modules\nf-core\adapterremoval\main.nf line 36:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\adapterremoval\main.nf line 37:

    $list \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$list" \

In .\modules\nf-core\adapterremoval\main.nf line 38:

    --basename ${prefix} \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --basename "${prefix}" \

In .\modules\nf-core\adapterremoval\main.nf line 39:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\adapterremoval\main.nf line 50:

ensure_fastq '${prefix}.truncated.gz'
             ^----------------------^ SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\adapterremoval\main.nf line 51:

ensure_fastq '${prefix}.discarded.gz'
             ^----------------------^ SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

For more information:
  https://www.shellcheck.net/wiki/SC2016 -- Expressions don't expand in singl...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\adapterremovalfixprefix\main.nf:

In .\modules\nf-core\adapterremovalfixprefix\main.nf line 28:

    $fastq \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fastq" \

In .\modules\nf-core\adapterremovalfixprefix\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\adapterremovalfixprefix\main.nf line 30:

    | gzip > ${prefix}.fq.gz
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | gzip > "${prefix}".fq.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\admixture\main.nf:

In .\modules\nf-core\admixture\main.nf line 28:

    $bed_ped_geno \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bed_ped_geno" \

In .\modules\nf-core\admixture\main.nf line 29:

    $K \
    ^-- SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$K" \

In .\modules\nf-core\admixture\main.nf line 30:

    -j$task.cpus \
      ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -j"$task".cpus \

In .\modules\nf-core\admixture\main.nf line 31:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\affy\justrma\main.nf:

In .\modules\nf-core\affy\justrma\main.nf line 30:

touch ${prefix}_eset.rds
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}"_eset.rds

In .\modules\nf-core\affy\justrma\main.nf line 31:

touch ${prefix}_matrix.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}"_matrix.tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\convertbed2gff\main.nf:

In .\modules\nf-core\agat\convertbed2gff\main.nf line 25:

    --bed $bed \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bed "$bed" \

In .\modules\nf-core\agat\convertbed2gff\main.nf line 26:

    --output ${prefix}.gff \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".gff \

In .\modules\nf-core\agat\convertbed2gff\main.nf line 27:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\convertspgff2gtf\main.nf:

In .\modules\nf-core\agat\convertspgff2gtf\main.nf line 26:

    --gff $gff \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gff "$gff" \

In .\modules\nf-core\agat\convertspgff2gtf\main.nf line 27:

    --output ${prefix}.agat.gtf \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".agat.gtf \

In .\modules\nf-core\agat\convertspgff2gtf\main.nf line 28:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\convertspgff2tsv\main.nf:

In .\modules\nf-core\agat\convertspgff2tsv\main.nf line 25:

    --gff $gff \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gff "$gff" \

In .\modules\nf-core\agat\convertspgff2tsv\main.nf line 26:

    --output ${prefix}.tsv \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".tsv \

In .\modules\nf-core\agat\convertspgff2tsv\main.nf line 27:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\convertspgxf2gxf\main.nf:

In .\modules\nf-core\agat\convertspgxf2gxf\main.nf line 26:

    --gxf $gxf \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gxf "$gxf" \

In .\modules\nf-core\agat\convertspgxf2gxf\main.nf line 27:

    --output ${prefix}.agat.gff \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".agat.gff \

In .\modules\nf-core\agat\convertspgxf2gxf\main.nf line 28:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\spaddintrons\main.nf:

In .\modules\nf-core\agat\spaddintrons\main.nf line 28:

    --gff $gff \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gff "$gff" \

In .\modules\nf-core\agat\spaddintrons\main.nf line 29:

    $config_param \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$config_param" \

In .\modules\nf-core\agat\spaddintrons\main.nf line 30:

    --out $output \
          ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --out "$output" \

In .\modules\nf-core\agat\spaddintrons\main.nf line 31:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\spextractsequences\main.nf:

In .\modules\nf-core\agat\spextractsequences\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\agat\spextractsequences\main.nf line 30:

    -g $gxf \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$gxf" \

In .\modules\nf-core\agat\spextractsequences\main.nf line 31:

    -f $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -f "$fasta" \

In .\modules\nf-core\agat\spextractsequences\main.nf line 32:

    $config_arg \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$config_arg" \

In .\modules\nf-core\agat\spextractsequences\main.nf line 33:

    -o ${prefix}.fasta
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".fasta

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\spfilterbyorfsize\main.nf:

In .\modules\nf-core\agat\spfilterbyorfsize\main.nf line 29:

    -g $gxf \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$gxf" \

In .\modules\nf-core\agat\spfilterbyorfsize\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\agat\spfilterbyorfsize\main.nf line 31:

    $config_arg \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$config_arg" \

In .\modules\nf-core\agat\spfilterbyorfsize\main.nf line 32:

    -o $prefix
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "$prefix"

In .\modules\nf-core\agat\spfilterbyorfsize\main.nf line 35:

    ${prefix}_NOT* \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"_NOT* \

In .\modules\nf-core\agat\spfilterbyorfsize\main.nf line 39:

    ${prefix}_* \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"_* \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\spfilterfeaturefromkilllist\main.nf:

In .\modules\nf-core\agat\spfilterfeaturefromkilllist\main.nf line 29:

    --gff $gff \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gff "$gff" \

In .\modules\nf-core\agat\spfilterfeaturefromkilllist\main.nf line 30:

    --kill_list $kill_list \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --kill_list "$kill_list" \

In .\modules\nf-core\agat\spfilterfeaturefromkilllist\main.nf line 31:

    $config_param \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$config_param" \

In .\modules\nf-core\agat\spfilterfeaturefromkilllist\main.nf line 32:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\spflagshortintrons\main.nf:

In .\modules\nf-core\agat\spflagshortintrons\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\agat\spflagshortintrons\main.nf line 29:

    -g $gxf \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$gxf" \

In .\modules\nf-core\agat\spflagshortintrons\main.nf line 30:

    $config_arg \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$config_arg" \

In .\modules\nf-core\agat\spflagshortintrons\main.nf line 31:

    -o ${prefix}.gff
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".gff

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\spkeeplongestisoform\main.nf:

In .\modules\nf-core\agat\spkeeplongestisoform\main.nf line 28:

    --gff $gxf \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gff "$gxf" \

In .\modules\nf-core\agat\spkeeplongestisoform\main.nf line 29:

    $config_param \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$config_param" \

In .\modules\nf-core\agat\spkeeplongestisoform\main.nf line 30:

    --out $output \
          ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --out "$output" \

In .\modules\nf-core\agat\spkeeplongestisoform\main.nf line 31:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\spmergeannotations\main.nf:

In .\modules\nf-core\agat\spmergeannotations\main.nf line 30:

    $gff_param \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gff_param" \

In .\modules\nf-core\agat\spmergeannotations\main.nf line 31:

    $config_param \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$config_param" \

In .\modules\nf-core\agat\spmergeannotations\main.nf line 32:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\agat\spmergeannotations\main.nf line 33:

    --output ${prefix}.gff
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".gff

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\spstatistics\main.nf:

In .\modules\nf-core\agat\spstatistics\main.nf line 25:

    --gff $gff \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gff "$gff" \

In .\modules\nf-core\agat\spstatistics\main.nf line 26:

    --output ${prefix}.stats.txt \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".stats.txt \

In .\modules\nf-core\agat\spstatistics\main.nf line 27:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agat\sqstatbasic\main.nf:

In .\modules\nf-core\agat\sqstatbasic\main.nf line 25:

    -i $gff \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$gff" \

In .\modules\nf-core\agat\sqstatbasic\main.nf line 26:

    --output ${prefix}.stats.txt \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".stats.txt \

In .\modules\nf-core\agat\sqstatbasic\main.nf line 27:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\agrvate\main.nf:

In .\modules\nf-core\agrvate\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\agrvate\main.nf line 27:

    -i $fasta
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$fasta"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ale\main.nf:

In .\modules\nf-core\ale\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ale\main.nf line 28:

    $bam \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam" \

In .\modules\nf-core\ale\main.nf line 29:

    $asm \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$asm" \

In .\modules\nf-core\ale\main.nf line 30:

    ${prefix}_ALEoutput.txt
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"_ALEoutput.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\allelecounter\main.nf:

In .\modules\nf-core\allelecounter\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\allelecounter\main.nf line 29:

    -l $loci \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -l "$loci" \

In .\modules\nf-core\allelecounter\main.nf line 30:

    -b $input \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "$input" \

In .\modules\nf-core\allelecounter\main.nf line 31:

    $reference_options \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference_options" \

In .\modules\nf-core\allelecounter\main.nf line 32:

    -o ${prefix}.alleleCount
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".alleleCount

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ampcombi\main.nf:

In .\modules\nf-core\ampcombi\main.nf line 50:

    --path_list '${amp_input.collect{"$it"}.join("' '")}' \
                ^-- SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\ampcombi\main.nf line 51:

    --sample_list ${prefix} \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --sample_list "${prefix}" \

In .\modules\nf-core\ampcombi\main.nf line 52:

    ${db} \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${db}" \

In .\modules\nf-core\ampcombi\main.nf line 53:

    --faa ${faa_input} \
          ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --faa "${faa_input}" \

In .\modules\nf-core\ampcombi\main.nf line 54:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ampcombi\main.nf line 56:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

For more information:
  https://www.shellcheck.net/wiki/SC2016 -- Expressions don't expand in singl...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ampcombi2\cluster\main.nf:

In .\modules\nf-core\ampcombi2\cluster\main.nf line 26:

    --ampcombi_summary ${summary_file} \
                       ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ampcombi_summary "${summary_file}" \

In .\modules\nf-core\ampcombi2\cluster\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ampcombi2\cluster\main.nf line 28:

    --threads ${task.cpus}
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ampcombi2\complete\main.nf:

In .\modules\nf-core\ampcombi2\complete\main.nf line 25:

    --summaries_files '${summaries.collect{"$it"}.join("' '")}' \
                      ^-- SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\ampcombi2\complete\main.nf line 26:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2016 -- Expressions don't expand in singl...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ampcombi2\parsetables\main.nf:

In .\modules\nf-core\ampcombi2\parsetables\main.nf line 43:

    --path_list '${amp_input.collect { "${it}" }.join("' '")}' \
                ^-- SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\ampcombi2\parsetables\main.nf line 44:

    --faa ${faa_input} \
          ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --faa "${faa_input}" \

In .\modules\nf-core\ampcombi2\parsetables\main.nf line 45:

    --gbk ${gbk_input} \
          ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gbk "${gbk_input}" \

In .\modules\nf-core\ampcombi2\parsetables\main.nf line 46:

    --sample_list ${prefix} \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --sample_list "${prefix}" \

In .\modules\nf-core\ampcombi2\parsetables\main.nf line 47:

    --amp_database ${opt_amp_db} \
                   ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --amp_database "${opt_amp_db}" \

In .\modules\nf-core\ampcombi2\parsetables\main.nf line 48:

    ${db_dir} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${db_dir}" \

In .\modules\nf-core\ampcombi2\parsetables\main.nf line 49:

    ${interpro} \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${interpro}" \

In .\modules\nf-core\ampcombi2\parsetables\main.nf line 50:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\ampcombi2\parsetables\main.nf line 51:

    --threads ${task.cpus}
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}"

For more information:
  https://www.shellcheck.net/wiki/SC2016 -- Expressions don't expand in singl...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ampir\main.nf:

In .\modules\nf-core\ampir\main.nf line 29:

#!/usr/bin/env Rscript
^-- SC1128 (error): The shebang must be on the first line. Delete blanks and move comments.

In .\modules\nf-core\ampir\main.nf line 30:

library(ampir)
^-- SC1073 (error): Couldn't parse this function. Fix to allow more checks.
        ^-- SC1065 (error): Trying to declare parameters? Don't. Use () and refer to params as $1, $2..

In .\modules\nf-core\ampir\main.nf line 32:

input_seqs <- read_faa('${faa}')
^-- SC1064 (error): Expected a { to open the function definition.
^-- SC1072 (error):  Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1064 -- Expected a { to open the function...
  https://www.shellcheck.net/wiki/SC1065 -- Trying to declare parameters? Don...
  https://www.shellcheck.net/wiki/SC1128 -- The shebang must be on the first ...

ShellCheck results for .\modules\nf-core\amplify\predict\main.nf:

In .\modules\nf-core\amplify\predict\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\amplify\predict\main.nf line 29:

    ${custom_model_dir} \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${custom_model_dir}" \

In .\modules\nf-core\amplify\predict\main.nf line 30:

    -s '${faa}'
       ^------^ SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\amplify\predict\main.nf line 33:

mv *.tsv ${prefix}.tsv
   ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv *.tsv "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2016 -- Expressions don't expand in singl...
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\amps\main.nf:

In .\modules\nf-core\amps\main.nf line 28:

    -r $maltextract_results \
       ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -r "$maltextract_results" \

In .\modules\nf-core\amps\main.nf line 29:

    -n $taxon_list \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -n "$taxon_list" \

In .\modules\nf-core\amps\main.nf line 30:

    -m $filter \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -m "$filter" \

In .\modules\nf-core\amps\main.nf line 31:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\amps\main.nf line 33:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\amrfinderplus\run\main.nf:

In .\modules\nf-core\amrfinderplus\run\main.nf line 39:

    gzip -c -d $fasta > $fasta_name
               ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "$fasta" > "$fasta_name"

In .\modules\nf-core\amrfinderplus\run\main.nf line 44:

    tar xzvf $db -C amrfinderdb
             ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    tar xzvf "$db" -C amrfinderdb

In .\modules\nf-core\amrfinderplus\run\main.nf line 46:

    mv $db amrfinderdb
       ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    mv "$db" amrfinderdb

In .\modules\nf-core\amrfinderplus\run\main.nf line 50:

    $fasta_param $fasta_name \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                 ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta_param" "$fasta_name" \

In .\modules\nf-core\amrfinderplus\run\main.nf line 51:

    $organism_param \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$organism_param" \

In .\modules\nf-core\amrfinderplus\run\main.nf line 52:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\amrfinderplus\run\main.nf line 54:

    --threads $task.cpus > ${prefix}.tsv
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus > "${prefix}".tsv

In .\modules\nf-core\amrfinderplus\run\main.nf line 56:

VER=\$(amrfinder --version)
^-^ SC2034 (warning): VER appears unused. Verify use (or export if used externally).
      ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
      ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- VER appears unused. Verify use (o...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...

ShellCheck results for .\modules\nf-core\amrfinderplus\update\main.nf:

In .\modules\nf-core\amrfinderplus\update\main.nf line 20:

tar czvf amrfinderdb.tar.gz -C amrfinderdb/\$(readlink amrfinderdb/latest) ./
                                             ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
                                             ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\amulety\antiberta2\main.nf:

In .\modules\nf-core\amulety\antiberta2\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\amulety\antiberta2\main.nf line 30:

    $tsv \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$tsv" \

In .\modules\nf-core\amulety\antiberta2\main.nf line 31:

    $chain \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$chain" \

In .\modules\nf-core\amulety\antiberta2\main.nf line 32:

    ${prefix}.tsv
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\amulety\antiberty\main.nf:

In .\modules\nf-core\amulety\antiberty\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\amulety\antiberty\main.nf line 29:

    $tsv \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$tsv" \

In .\modules\nf-core\amulety\antiberty\main.nf line 30:

    $chain \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$chain" \

In .\modules\nf-core\amulety\antiberty\main.nf line 31:

    ${prefix}.tsv
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\amulety\balmpaired\main.nf:

In .\modules\nf-core\amulety\balmpaired\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\amulety\balmpaired\main.nf line 29:

    $tsv \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$tsv" \

In .\modules\nf-core\amulety\balmpaired\main.nf line 30:

    $chain \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$chain" \

In .\modules\nf-core\amulety\balmpaired\main.nf line 31:

    ${prefix}.tsv
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\amulety\esm2\main.nf:

In .\modules\nf-core\amulety\esm2\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\amulety\esm2\main.nf line 29:

    $tsv \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$tsv" \

In .\modules\nf-core\amulety\esm2\main.nf line 30:

    $chain \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$chain" \

In .\modules\nf-core\amulety\esm2\main.nf line 31:

    ${prefix}.tsv
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\amulety\translate\main.nf:

In .\modules\nf-core\amulety\translate\main.nf line 26:

amulety translate-igblast $tsv . ${reference_igblast}
                          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
amulety translate-igblast "$tsv" . "${reference_igblast}"

In .\modules\nf-core\amulety\translate\main.nf line 28:

mv *_translated.tsv ${prefix}_translated.tsv
   ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv *_translated.tsv "${prefix}"_translated.tsv

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\angsd\contamination\main.nf:

In .\modules\nf-core\angsd\contamination\main.nf line 26:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\angsd\contamination\main.nf line 27:

    -a ${icounts} \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -a "${icounts}" \

In .\modules\nf-core\angsd\contamination\main.nf line 28:

    -h ${hapmap_file} \
       ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -h "${hapmap_file}" \

In .\modules\nf-core\angsd\contamination\main.nf line 29:

    -p ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${task.cpus}" \

In .\modules\nf-core\angsd\contamination\main.nf line 30:

    2> >(tee ${prefix}.txt >&2)
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    2> >(tee "${prefix}".txt >&2)

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\angsd\docounts\main.nf:

In .\modules\nf-core\angsd\docounts\main.nf line 30:

ls -1 *.bam > bamlist.txt
      ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.

In .\modules\nf-core\angsd\docounts\main.nf line 33:

    -nThreads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -nThreads "${task.cpus}" \

In .\modules\nf-core\angsd\docounts\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\angsd\docounts\main.nf line 37:

    -out ${prefix} \
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -out "${prefix}" \

In .\modules\nf-core\angsd\docounts\main.nf line 38:

    $minq
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$minq"

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\angsd\gl\main.nf:

In .\modules\nf-core\angsd\gl\main.nf line 33:

ls -1 *.bam > bamlist.txt
      ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.

In .\modules\nf-core\angsd\gl\main.nf line 36:

    -nThreads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -nThreads "${task.cpus}" \

In .\modules\nf-core\angsd\gl\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\angsd\gl\main.nf line 39:

    $ref \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ref" \

In .\modules\nf-core\angsd\gl\main.nf line 40:

    $output_mode \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$output_mode" \

In .\modules\nf-core\angsd\gl\main.nf line 41:

    -out ${prefix}
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -out "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\anndata\barcodes\main.nf:

In .\modules\nf-core\anndata\barcodes\main.nf line 27:

touch ${prefix}.h5ad
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".h5ad

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\anndata\getsize\main.nf:

In .\modules\nf-core\anndata\getsize\main.nf line 28:

touch ${prefix}.txt
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\annosine\main.nf:

In .\modules\nf-core\annosine\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\annosine\main.nf line 31:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\annosine\main.nf line 32:

    $mode \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$mode" \

In .\modules\nf-core\annosine\main.nf line 33:

    $fasta \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" \

In .\modules\nf-core\annosine\main.nf line 34:

    $prefix \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$prefix" \

In .\modules\nf-core\annosine\main.nf line 35:

    &> >(tee ${prefix}.log 2>&1)
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    &> >(tee "${prefix}".log 2>&1)

In .\modules\nf-core\annosine\main.nf line 38:

    $prefix/Seed_SINE.fa \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$prefix"/Seed_SINE.fa \

In .\modules\nf-core\annosine\main.nf line 39:

    ${prefix}.fa \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".fa \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\annotsv\annotsv\main.nf:

In .\modules\nf-core\annotsv\annotsv\main.nf line 37:

    -annotationsDir ${annotations} \
                    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -annotationsDir "${annotations}" \

In .\modules\nf-core\annotsv\annotsv\main.nf line 38:

    ${cand_genes} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${cand_genes}" \

In .\modules\nf-core\annotsv\annotsv\main.nf line 39:

    ${small_variants} \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${small_variants}" \

In .\modules\nf-core\annotsv\annotsv\main.nf line 40:

    ${fp_snv} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fp_snv}" \

In .\modules\nf-core\annotsv\annotsv\main.nf line 41:

    ${transcripts} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${transcripts}" \

In .\modules\nf-core\annotsv\annotsv\main.nf line 42:

    -outputFile ${prefix}.tsv \
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -outputFile "${prefix}".tsv \

In .\modules\nf-core\annotsv\annotsv\main.nf line 43:

    -SVinputFile ${sv_vcf} \
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -SVinputFile "${sv_vcf}" \

In .\modules\nf-core\annotsv\annotsv\main.nf line 44:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

In .\modules\nf-core\annotsv\annotsv\main.nf line 46:

mv *_AnnotSV/* .
   ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\antismash\antismashlite\main.nf:

In .\modules\nf-core\antismash\antismashlite\main.nf line 57:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\antismash\antismashlite\main.nf line 58:

    ${gff_flag} \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${gff_flag}" \

In .\modules\nf-core\antismash\antismashlite\main.nf line 59:

    -c ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -c "${task.cpus}" \

In .\modules\nf-core\antismash\antismashlite\main.nf line 60:

    --output-dir ${prefix} \
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-dir "${prefix}" \

In .\modules\nf-core\antismash\antismashlite\main.nf line 61:

    --output-basename ${prefix} \
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-basename "${prefix}" \

In .\modules\nf-core\antismash\antismashlite\main.nf line 63:

    --logfile ${prefix}/${prefix}.log \
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --logfile "${prefix}"/"${prefix}".log \

In .\modules\nf-core\antismash\antismashlite\main.nf line 64:

    --databases ${databases} \
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --databases "${databases}" \

In .\modules\nf-core\antismash\antismashlite\main.nf line 65:

    ${sequence_input}
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${sequence_input}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\antismash\antismashlitedownloaddatabases\main.nf:

In .\modules\nf-core\antismash\antismashlitedownloaddatabases\main.nf line 42:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\arcashla\extract\main.nf:

In .\modules\nf-core\arcashla\extract\main.nf line 33:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\arcashla\extract\main.nf line 34:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\arcashla\extract\main.nf line 37:

    --log ${prefix}.log \
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --log "${prefix}".log \

In .\modules\nf-core\arcashla\extract\main.nf line 38:

    $single_end \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$single_end" \

In .\modules\nf-core\arcashla\extract\main.nf line 39:

    $bam
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\argnorm\main.nf:

In .\modules\nf-core\argnorm\main.nf line 34:

    ${tool} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${tool}" \

In .\modules\nf-core\argnorm\main.nf line 35:

    -i ${input_tsv} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${input_tsv}" \

In .\modules\nf-core\argnorm\main.nf line 36:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\argnorm\main.nf line 37:

    ${db_args} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${db_args}" \

In .\modules\nf-core\argnorm\main.nf line 38:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\aria2\main.nf:

In .\modules\nf-core\aria2\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\aria2\main.nf line 28:

    $source_url
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$source_url"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ariba\getref\main.nf:

In .\modules\nf-core\ariba\getref\main.nf line 25:

    ${db_name} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${db_name}" \

In .\modules\nf-core\ariba\getref\main.nf line 26:

    ${db_name}
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${db_name}"

In .\modules\nf-core\ariba\getref\main.nf line 30:

    -f ${db_name}.fa \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -f "${db_name}".fa \

In .\modules\nf-core\ariba\getref\main.nf line 31:

    -m ${db_name}.tsv \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -m "${db_name}".tsv \

In .\modules\nf-core\ariba\getref\main.nf line 32:

    ${db_name}
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${db_name}"

In .\modules\nf-core\ariba\getref\main.nf line 34:

tar -zcvf ${db_name}.tar.gz ${db_name}/
          ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                            ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
tar -zcvf "${db_name}".tar.gz "${db_name}"/

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ariba\run\main.nf:

In .\modules\nf-core\ariba\run\main.nf line 26:

tar -xzvf ${db}
          ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
tar -xzvf "${db}"

In .\modules\nf-core\ariba\run\main.nf line 29:

    ${db_name}/ \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${db_name}"/ \

In .\modules\nf-core\ariba\run\main.nf line 30:

    ${reads} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reads}" \

In .\modules\nf-core\ariba\run\main.nf line 31:

    ${prefix} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}" \

In .\modules\nf-core\ariba\run\main.nf line 32:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ariba\run\main.nf line 33:

    --threads $task.cpus
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\arriba\arriba\main.nf:

In .\modules\nf-core\arriba\arriba\main.nf line 37:

    -x $bam \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -x "$bam" \

In .\modules\nf-core\arriba\arriba\main.nf line 38:

    -a $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -a "$fasta" \

In .\modules\nf-core\arriba\arriba\main.nf line 39:

    -g $gtf \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$gtf" \

In .\modules\nf-core\arriba\arriba\main.nf line 40:

    -o ${prefix}.fusions.tsv \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".fusions.tsv \

In .\modules\nf-core\arriba\arriba\main.nf line 41:

    -O ${prefix}.fusions.discarded.tsv \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -O "${prefix}".fusions.discarded.tsv \

In .\modules\nf-core\arriba\arriba\main.nf line 42:

    $blacklist_arg \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$blacklist_arg" \

In .\modules\nf-core\arriba\arriba\main.nf line 43:

    $known_fusions_arg \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$known_fusions_arg" \

In .\modules\nf-core\arriba\arriba\main.nf line 44:

    $cytobands_arg \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$cytobands_arg" \

In .\modules\nf-core\arriba\arriba\main.nf line 45:

    $protein_domains_arg \
    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$protein_domains_arg" \

In .\modules\nf-core\arriba\arriba\main.nf line 46:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\art\illumina\main.nf:

In .\modules\nf-core\art\illumina\main.nf line 34:

    -ss $sequencing_system \
        ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -ss "$sequencing_system" \

In .\modules\nf-core\art\illumina\main.nf line 35:

    -i $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$fasta" \

In .\modules\nf-core\art\illumina\main.nf line 36:

    -l $read_length \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -l "$read_length" \

In .\modules\nf-core\art\illumina\main.nf line 37:

    -f $fold_coverage \
       ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -f "$fold_coverage" \

In .\modules\nf-core\art\illumina\main.nf line 38:

    -o $prefix \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "$prefix" \

In .\modules\nf-core\art\illumina\main.nf line 39:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

In .\modules\nf-core\art\illumina\main.nf line 43:

    $args2 \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2" \

In .\modules\nf-core\art\illumina\main.nf line 44:

    $prefix*.fq
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$prefix"*.fq

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\artic\guppyplex\main.nf:

In .\modules\nf-core\artic\guppyplex\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\artic\guppyplex\main.nf line 27:

    --directory $fastq_dir \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --directory "$fastq_dir" \

In .\modules\nf-core\artic\guppyplex\main.nf line 28:

    --output ${prefix}.fastq
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".fastq

In .\modules\nf-core\artic\guppyplex\main.nf line 30:

pigz -p $task.cpus *.fastq
        ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                   ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.

Did you mean: 
pigz -p "$task".cpus *.fastq

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\artic\minion\main.nf:

In .\modules\nf-core\artic\minion\main.nf line 42:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\artic\minion\main.nf line 43:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\artic\minion\main.nf line 44:

    --read-file $fastq \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --read-file "$fastq" \

In .\modules\nf-core\artic\minion\main.nf line 45:

    --bed $bed \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bed "$bed" \

In .\modules\nf-core\artic\minion\main.nf line 46:

    --ref $fasta \
          ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ref "$fasta" \

In .\modules\nf-core\artic\minion\main.nf line 47:

    $model_dir_cmd \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$model_dir_cmd" \

In .\modules\nf-core\artic\minion\main.nf line 48:

    --model $model \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --model "$model" \

In .\modules\nf-core\artic\minion\main.nf line 49:

    $prefix
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$prefix"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ascat\main.nf:

In .\modules\nf-core\ascat\main.nf line 53:

#!/usr/bin/env Rscript
^-- SC1128 (error): The shebang must be on the first line. Delete blanks and move comments.

In .\modules\nf-core\ascat\main.nf line 54:

library(RColorBrewer)
^-- SC1073 (error): Couldn't parse this function. Fix to allow more checks.
        ^-- SC1065 (error): Trying to declare parameters? Don't. Use () and refer to params as $1, $2..

In .\modules\nf-core\ascat\main.nf line 55:

library(ASCAT)
^-- SC1064 (error): Expected a { to open the function definition.
^-- SC1072 (error):  Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1064 -- Expected a { to open the function...
  https://www.shellcheck.net/wiki/SC1065 -- Trying to declare parameters? Don...
  https://www.shellcheck.net/wiki/SC1128 -- The shebang must be on the first ...

ShellCheck results for .\modules\nf-core\ashlar\main.nf:

In .\modules\nf-core\ashlar\main.nf line 39:

    -o ${prefix}.ome.tif \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".ome.tif \

In .\modules\nf-core\ashlar\main.nf line 40:

    $images \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$images" \

In .\modules\nf-core\ashlar\main.nf line 41:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ashlar\main.nf line 42:

    $dfp \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$dfp" \

In .\modules\nf-core\ashlar\main.nf line 43:

    $ffp
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ffp"

In .\modules\nf-core\ashlar\main.nf line 45:

sed -i -E 's/UUID="urn:uuid:[[:xdigit:]]{8}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{12}"/                                                    /g' ${prefix}.ome.tif
                                                                                                                                                                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
sed -i -E 's/UUID="urn:uuid:[[:xdigit:]]{8}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{4}-[[:xdigit:]]{12}"/                                                    /g' "${prefix}".ome.tif

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\assemblyscan\main.nf:

In .\modules\nf-core\assemblyscan\main.nf line 24:

assembly-scan $assembly > ${prefix}.json
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
assembly-scan "$assembly" > "${prefix}".json

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ataqv\ataqv\main.nf:

In .\modules\nf-core\ataqv\ataqv\main.nf line 36:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ataqv\ataqv\main.nf line 37:

    $mito \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$mito" \

In .\modules\nf-core\ataqv\ataqv\main.nf line 38:

    $peak \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$peak" \

In .\modules\nf-core\ataqv\ataqv\main.nf line 39:

    $tss \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$tss" \

In .\modules\nf-core\ataqv\ataqv\main.nf line 40:

    $excl_regs \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$excl_regs" \

In .\modules\nf-core\ataqv\ataqv\main.nf line 41:

    $autosom_ref \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$autosom_ref" \

In .\modules\nf-core\ataqv\ataqv\main.nf line 43:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\ataqv\ataqv\main.nf line 44:

    --name $prefix \
           ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --name "$prefix" \

In .\modules\nf-core\ataqv\ataqv\main.nf line 45:

    $organism \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$organism" \

In .\modules\nf-core\ataqv\ataqv\main.nf line 46:

    $bam
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ataqv\mkarv\main.nf:

In .\modules\nf-core\ataqv\mkarv\main.nf line 23:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ataqv\mkarv\main.nf line 24:

    --concurrency $task.cpus \
                  ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --concurrency "$task".cpus \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\atlas\call\main.nf:

In .\modules\nf-core\atlas\call\main.nf line 37:

    bam=${bam} \
        ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    bam="${bam}" \

In .\modules\nf-core\atlas\call\main.nf line 38:

    fasta=${fasta} \
          ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    fasta="${fasta}" \

In .\modules\nf-core\atlas\call\main.nf line 39:

    $recal_file \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$recal_file" \

In .\modules\nf-core\atlas\call\main.nf line 40:

    $pmd_file \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$pmd_file" \

In .\modules\nf-core\atlas\call\main.nf line 41:

    $known_alleles_file \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$known_alleles_file" \

In .\modules\nf-core\atlas\call\main.nf line 42:

    method=${method} \
           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    method="${method}" \

In .\modules\nf-core\atlas\call\main.nf line 43:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\atlas\pmd\main.nf:

In .\modules\nf-core\atlas\pmd\main.nf line 31:

    $pool_rg_txt \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$pool_rg_txt" \

In .\modules\nf-core\atlas\pmd\main.nf line 33:

    bam=${bam} \
        ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    bam="${bam}" \

In .\modules\nf-core\atlas\pmd\main.nf line 34:

    fasta=${fasta} \
          ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    fasta="${fasta}" \

In .\modules\nf-core\atlas\pmd\main.nf line 35:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\atlas\recal\main.nf:

In .\modules\nf-core\atlas\recal\main.nf line 33:

    bam=$bam \
        ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    bam="$bam" \

In .\modules\nf-core\atlas\recal\main.nf line 34:

    $PMD \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$PMD" \

In .\modules\nf-core\atlas\recal\main.nf line 35:

    $READGROUPS \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$READGROUPS" \

In .\modules\nf-core\atlas\recal\main.nf line 36:

    $ALLELES \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ALLELES" \

In .\modules\nf-core\atlas\recal\main.nf line 37:

    $INVARIANTS \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$INVARIANTS" \

In .\modules\nf-core\atlas\recal\main.nf line 38:

    out=$prefix \
        ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    out="$prefix" \

In .\modules\nf-core\atlas\recal\main.nf line 39:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\atlas\splitmerge\main.nf:

In .\modules\nf-core\atlas\splitmerge\main.nf line 27:

    task=splitMerge bam=${bam} \
                        ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    task=splitMerge bam="${bam}" \

In .\modules\nf-core\atlas\splitmerge\main.nf line 28:

    readGroupSettings=${read_group_settings}\
                      ^--------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    readGroupSettings="${read_group_settings}"\

In .\modules\nf-core\atlas\splitmerge\main.nf line 29:

    $optional \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$optional" \

In .\modules\nf-core\atlas\splitmerge\main.nf line 30:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\atlasgeneannotationmanipulation\gtf2featureannotation\main.nf:

In .\modules\nf-core\atlasgeneannotationmanipulation\gtf2featureannotation\main.nf line 30:

    --gtf-file $gtf \
               ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gtf-file "$gtf" \

In .\modules\nf-core\atlasgeneannotationmanipulation\gtf2featureannotation\main.nf line 31:

    --output-file ${prefix}.anno.tsv \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-file "${prefix}".anno.tsv \

In .\modules\nf-core\atlasgeneannotationmanipulation\gtf2featureannotation\main.nf line 32:

    $reference_cdna \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference_cdna" \

In .\modules\nf-core\atlasgeneannotationmanipulation\gtf2featureannotation\main.nf line 33:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\authentict\deam2cont\main.nf:

In .\modules\nf-core\authentict\deam2cont\main.nf line 30:

samtools view $args $bam | AuthentiCT \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
samtools view "$args" "$bam" | AuthentiCT \

In .\modules\nf-core\authentict\deam2cont\main.nf line 32:

    $args2 \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2" \

In .\modules\nf-core\authentict\deam2cont\main.nf line 33:

    $config_file \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$config_file" \

In .\modules\nf-core\authentict\deam2cont\main.nf line 34:

    $positions_file \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$positions_file" \

In .\modules\nf-core\authentict\deam2cont\main.nf line 36:

    > ${prefix}.txt
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\backsub\main.nf:

In .\modules\nf-core\backsub\main.nf line 32:

    -r $image \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -r "$image" \

In .\modules\nf-core\backsub\main.nf line 33:

    -m $markerfile \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -m "$markerfile" \

In .\modules\nf-core\backsub\main.nf line 34:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bacphlip\main.nf:

In .\modules\nf-core\bacphlip\main.nf line 27:

    -i $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$fasta" \

In .\modules\nf-core\bacphlip\main.nf line 28:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bakta\bakta\main.nf:

In .\modules\nf-core\bakta\bakta\main.nf line 39:

    $fasta \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" \

In .\modules\nf-core\bakta\bakta\main.nf line 40:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bakta\bakta\main.nf line 41:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bakta\bakta\main.nf line 42:

    --prefix $prefix \
             ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --prefix "$prefix" \

In .\modules\nf-core\bakta\bakta\main.nf line 43:

    $proteins_opt \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$proteins_opt" \

In .\modules\nf-core\bakta\bakta\main.nf line 44:

    $prodigal_tf \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$prodigal_tf" \

In .\modules\nf-core\bakta\bakta\main.nf line 45:

    --db $db
         ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --db "$db"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bakta\baktadbdownload\main.nf:

In .\modules\nf-core\bakta\baktadbdownload\main.nf line 21:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bam2fastx\bam2fastq\main.nf:

In .\modules\nf-core\bam2fastx\bam2fastq\main.nf line 33:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bam2fastx\bam2fastq\main.nf line 34:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\bam2fastx\bam2fastq\main.nf line 35:

    $bam
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bamaligncleaner\main.nf:

In .\modules\nf-core\bamaligncleaner\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bamaligncleaner\main.nf line 27:

    -o ${prefix}.bam \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".bam \

In .\modules\nf-core\bamaligncleaner\main.nf line 28:

    ${bam}
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bam}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bamclipper\main.nf:

In .\modules\nf-core\bamclipper\main.nf line 28:

    -b ${bam} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "${bam}" \

In .\modules\nf-core\bamclipper\main.nf line 29:

    -p ${bedpe} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${bedpe}" \

In .\modules\nf-core\bamclipper\main.nf line 30:

    -n $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -n "$task".cpus \

In .\modules\nf-core\bamclipper\main.nf line 31:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bamcmp\main.nf:

In .\modules\nf-core\bamcmp\main.nf line 42:

    -1 $primary_aligned_bam \
       ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -1 "$primary_aligned_bam" \

In .\modules\nf-core\bamcmp\main.nf line 43:

    -2 $contaminant_aligned_bam \
       ^----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -2 "$contaminant_aligned_bam" \

In .\modules\nf-core\bamcmp\main.nf line 44:

    -A ${prefix}.bam \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -A "${prefix}".bam \

In .\modules\nf-core\bamcmp\main.nf line 45:

    -B ${prefix2}.bam \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -B "${prefix2}".bam \

In .\modules\nf-core\bamcmp\main.nf line 46:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bamstats\generalstats\main.nf:

In .\modules\nf-core\bamstats\generalstats\main.nf line 27:

    -i $bam \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bam" \

In .\modules\nf-core\bamstats\generalstats\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bamstats\generalstats\main.nf line 29:

    -c $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -c "$task".cpus \

In .\modules\nf-core\bamstats\generalstats\main.nf line 30:

    -o ${prefix}.json
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".json

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bamtofastq10x\main.nf:

In .\modules\nf-core\bamtofastq10x\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bamtofastq10x\main.nf line 26:

    $bam \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam" \

In .\modules\nf-core\bamtofastq10x\main.nf line 27:

    $prefix
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$prefix"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bamtools\convert\main.nf:

In .\modules\nf-core\bamtools\convert\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bamtools\convert\main.nf line 32:

    -in $bam \
        ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -in "$bam" \

In .\modules\nf-core\bamtools\convert\main.nf line 33:

    -out ${prefix}.${extension}
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                   ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -out "${prefix}"."${extension}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bamtools\split\main.nf:

In .\modules\nf-core\bamtools\split\main.nf line 27:

    $input_list \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_list" \

In .\modules\nf-core\bamtools\split\main.nf line 30:

        -stub $prefix \
              ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        -stub "$prefix" \

In .\modules\nf-core\bamtools\split\main.nf line 31:

        $args
        ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bamtools\stats\main.nf:

In .\modules\nf-core\bamtools\stats\main.nf line 26:

    -in $bam \
        ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -in "$bam" \

In .\modules\nf-core\bamtools\stats\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bamtools\stats\main.nf line 28:

    >${prefix}.bam.stats
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    >"${prefix}".bam.stats

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bamutil\trimbam\main.nf:

In .\modules\nf-core\bamutil\trimbam\main.nf line 26:

    $bam \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam" \

In .\modules\nf-core\bamutil\trimbam\main.nf line 27:

    ${prefix}.bam \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".bam \

In .\modules\nf-core\bamutil\trimbam\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bamutil\trimbam\main.nf line 29:

    -L $trim_left \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -L "$trim_left" \

In .\modules\nf-core\bamutil\trimbam\main.nf line 30:

    -R $trim_right
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -R "$trim_right"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bandage\image\main.nf:

In .\modules\nf-core\bandage\image\main.nf line 25:

Bandage image $gfa ${prefix}.png $args
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.
                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
Bandage image "$gfa" "${prefix}".png "$args"

In .\modules\nf-core\bandage\image\main.nf line 26:

Bandage image $gfa ${prefix}.svg $args
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.
                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
Bandage image "$gfa" "${prefix}".svg "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\barrnap\main.nf:

In .\modules\nf-core\barrnap\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\barrnap\main.nf line 32:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\barrnap\main.nf line 33:

    --kingdom $db \
              ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --kingdom "$db" \

In .\modules\nf-core\barrnap\main.nf line 34:

    $input \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" \

In .\modules\nf-core\barrnap\main.nf line 35:

    > ${prefix}_${db}.gff
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"_"${db}".gff

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bases2fastq\main.nf:

In .\modules\nf-core\bases2fastq\main.nf line 33:

    -p $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "$task".cpus \

In .\modules\nf-core\bases2fastq\main.nf line 34:

    $runManifest \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$runManifest" \

In .\modules\nf-core\bases2fastq\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bases2fastq\main.nf line 36:

    $run_dir \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$run_dir" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\basicpy\main.nf:

In .\modules\nf-core\basicpy\main.nf line 25:

/opt/main.py -i $image -o . $args
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                            ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
/opt/main.py -i "$image" -o . "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bbmap\align\main.nf:

In .\modules\nf-core\bbmap\align\main.nf line 43:

    $db \
    ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$db" \

In .\modules\nf-core\bbmap\align\main.nf line 44:

    $input \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" \

In .\modules\nf-core\bbmap\align\main.nf line 45:

    out=${prefix}.bam \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    out="${prefix}".bam \

In .\modules\nf-core\bbmap\align\main.nf line 46:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bbmap\align\main.nf line 47:

    threads=$task.cpus \
            ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    threads="$task".cpus \

In .\modules\nf-core\bbmap\align\main.nf line 48:

    -Xmx${task.memory.toGiga()}g \
        ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${task.memory.toGiga()}"g \

In .\modules\nf-core\bbmap\align\main.nf line 49:

    &> ${prefix}.bbmap.log
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    &> "${prefix}".bbmap.log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bbmap\bbduk\main.nf:

In .\modules\nf-core\bbmap\bbduk\main.nf line 29:

maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g')
^----^ SC2034 (warning): maxmem appears unused. Verify use (or export if used externally).
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- maxmem appears unused. Verify use...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\bbmap\bbmerge\main.nf:

In .\modules\nf-core\bbmap\bbmerge\main.nf line 30:

maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g')
^----^ SC2034 (warning): maxmem appears unused. Verify use (or export if used externally).
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- maxmem appears unused. Verify use...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\bbmap\bbnorm\main.nf:

In .\modules\nf-core\bbmap\bbnorm\main.nf line 37:

    $input \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" \

In .\modules\nf-core\bbmap\bbnorm\main.nf line 38:

    $output \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$output" \

In .\modules\nf-core\bbmap\bbnorm\main.nf line 39:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bbmap\bbnorm\main.nf line 40:

    threads=$task.cpus \
            ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    threads="$task".cpus \

In .\modules\nf-core\bbmap\bbnorm\main.nf line 41:

    $memory \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$memory" \

In .\modules\nf-core\bbmap\bbnorm\main.nf line 42:

    &> ${prefix}.bbnorm.log
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    &> "${prefix}".bbnorm.log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bbmap\bbsplit\main.nf:

In .\modules\nf-core\bbmap\bbsplit\main.nf line 74:

if [ $index ]; then
               ^-- SC1009 (info): The mentioned syntax error was in this then clause.

In .\modules\nf-core\bbmap\bbsplit\main.nf line 75:

    for summary_file in \$(find $index/ref/genome -name summary.txt); do
    ^-- SC1073 (error): Couldn't parse this for loop. Fix to allow more checks.
                          ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
                          ^-- SC1058 (error): Expected 'do'.
                          ^-- SC1072 (error): Expected 'do'. Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1058 -- Expected 'do'.
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1072 -- Expected 'do'. Fix any mentioned ...

ShellCheck results for .\modules\nf-core\bbmap\clumpify\main.nf:

In .\modules\nf-core\bbmap\clumpify\main.nf line 29:

    $raw \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$raw" \

In .\modules\nf-core\bbmap\clumpify\main.nf line 30:

    $clumped \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$clumped" \

In .\modules\nf-core\bbmap\clumpify\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bbmap\clumpify\main.nf line 32:

    &> ${prefix}.clumpify.log
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    &> "${prefix}".clumpify.log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bbmap\filterbyname\main.nf:

In .\modules\nf-core\bbmap\filterbyname\main.nf line 42:

    -Xmx${avail_mem}g \
        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${avail_mem}"g \

In .\modules\nf-core\bbmap\filterbyname\main.nf line 43:

    $input \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" \

In .\modules\nf-core\bbmap\filterbyname\main.nf line 44:

    $output \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$output" \

In .\modules\nf-core\bbmap\filterbyname\main.nf line 45:

    $names_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$names_command" \

In .\modules\nf-core\bbmap\filterbyname\main.nf line 46:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bbmap\filterbyname\main.nf line 47:

    | tee ${prefix}.log
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | tee "${prefix}".log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bbmap\index\main.nf:

In .\modules\nf-core\bbmap\index\main.nf line 24:

    ref=${fasta} \
        ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    ref="${fasta}" \

In .\modules\nf-core\bbmap\index\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bbmap\index\main.nf line 26:

    threads=$task.cpus \
            ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    threads="$task".cpus \

In .\modules\nf-core\bbmap\index\main.nf line 27:

    -Xmx${task.memory.toGiga()}g
        ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${task.memory.toGiga()}"g

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bbmap\pileup\main.nf:

In .\modules\nf-core\bbmap\pileup\main.nf line 26:

    -Xmx${task.memory.toGiga()}g \
        ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${task.memory.toGiga()}"g \

In .\modules\nf-core\bbmap\pileup\main.nf line 27:

    in=${bam} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    in="${bam}" \

In .\modules\nf-core\bbmap\pileup\main.nf line 28:

    out=${prefix}.coverage.stats.txt \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    out="${prefix}".coverage.stats.txt \

In .\modules\nf-core\bbmap\pileup\main.nf line 29:

    hist=${prefix}.coverage.hist.txt \
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    hist="${prefix}".coverage.hist.txt \

In .\modules\nf-core\bbmap\pileup\main.nf line 30:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bbmap\repair\main.nf:

In .\modules\nf-core\bbmap\repair\main.nf line 29:

maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g')
^----^ SC2034 (warning): maxmem appears unused. Verify use (or export if used externally).
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- maxmem appears unused. Verify use...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\bbmap\sendsketch\main.nf:

In .\modules\nf-core\bbmap\sendsketch\main.nf line 31:

sendsketch.sh -Xmx${avail_mem}M \
                  ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
sendsketch.sh -Xmx"${avail_mem}"M \

In .\modules\nf-core\bbmap\sendsketch\main.nf line 32:

    in=${file_used} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    in="${file_used}" \

In .\modules\nf-core\bbmap\sendsketch\main.nf line 33:

    out=${prefix}.txt \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    out="${prefix}".txt \

In .\modules\nf-core\bbmap\sendsketch\main.nf line 34:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\annotate\main.nf:

In .\modules\nf-core\bcftools\annotate\main.nf line 43:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\annotate\main.nf line 44:

    $annotations_file \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$annotations_file" \

In .\modules\nf-core\bcftools\annotate\main.nf line 45:

    $rename_chrs_file \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$rename_chrs_file" \

In .\modules\nf-core\bcftools\annotate\main.nf line 46:

    $header_file \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$header_file" \

In .\modules\nf-core\bcftools\annotate\main.nf line 47:

    --output ${prefix}.${extension} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}" \

In .\modules\nf-core\bcftools\annotate\main.nf line 48:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\annotate\main.nf line 49:

    $input
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\call\main.nf:

In .\modules\nf-core\bcftools\call\main.nf line 33:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\bcftools\call\main.nf line 34:

    ${regions_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions_file}" \

In .\modules\nf-core\bcftools\call\main.nf line 35:

    ${targets_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${targets_file}" \

In .\modules\nf-core\bcftools\call\main.nf line 36:

    ${samples_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${samples_file}" \

In .\modules\nf-core\bcftools\call\main.nf line 37:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\call\main.nf line 38:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\call\main.nf line 39:

    ${vcf}
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcf}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\concat\main.nf:

In .\modules\nf-core\bcftools\concat\main.nf line 36:

    --output ${prefix}.${extension} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}" \

In .\modules\nf-core\bcftools\concat\main.nf line 37:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\concat\main.nf line 38:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\concat\main.nf line 39:

    ${vcfs}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcfs}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\consensus\main.nf:

In .\modules\nf-core\bcftools\consensus\main.nf line 25:

cat $fasta \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
cat "$fasta" \

In .\modules\nf-core\bcftools\consensus\main.nf line 28:

        $vcf \
        ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "$vcf" \

In .\modules\nf-core\bcftools\consensus\main.nf line 29:

        $args \
        ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "$args" \

In .\modules\nf-core\bcftools\consensus\main.nf line 30:

        $masking \
        ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "$masking" \

In .\modules\nf-core\bcftools\consensus\main.nf line 31:

        > ${prefix}.fa
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        > "${prefix}".fa

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\convert\main.nf:

In .\modules\nf-core\bcftools\convert\main.nf line 49:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\convert\main.nf line 50:

    $regions \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$regions" \

In .\modules\nf-core\bcftools\convert\main.nf line 51:

    $output_cmd \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$output_cmd" \

In .\modules\nf-core\bcftools\convert\main.nf line 52:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\convert\main.nf line 53:

    $reference \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference" \

In .\modules\nf-core\bcftools\convert\main.nf line 54:

    $input
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\csq\main.nf:

In .\modules\nf-core\bcftools\csq\main.nf line 37:

    --output ${prefix}.${extension} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}" \

In .\modules\nf-core\bcftools\csq\main.nf line 38:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\bcftools\csq\main.nf line 39:

    --fasta-ref ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fasta-ref "${fasta}" \

In .\modules\nf-core\bcftools\csq\main.nf line 40:

    --gff-annot ${gff3} \
                ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gff-annot "${gff3}" \

In .\modules\nf-core\bcftools\csq\main.nf line 41:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\csq\main.nf line 42:

    $vcf
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\filter\main.nf:

In .\modules\nf-core\bcftools\filter\main.nf line 36:

    --output ${prefix}.${extension} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}" \

In .\modules\nf-core\bcftools\filter\main.nf line 37:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\bcftools\filter\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\filter\main.nf line 39:

    $vcf
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\index\main.nf:

In .\modules\nf-core\bcftools\index\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\index\main.nf line 29:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\index\main.nf line 30:

    $vcf
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\isec\main.nf:

In .\modules\nf-core\bcftools\isec\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\isec\main.nf line 26:

    -p $prefix \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "$prefix" \

In .\modules\nf-core\bcftools\isec\main.nf line 27:

    ${vcfs}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcfs}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\merge\main.nf:

In .\modules\nf-core\bcftools\merge\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\merge\main.nf line 39:

    $regions \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$regions" \

In .\modules\nf-core\bcftools\merge\main.nf line 40:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\merge\main.nf line 41:

    --output ${prefix}.${extension} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}" \

In .\modules\nf-core\bcftools\merge\main.nf line 42:

    $input
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\mpileup\main.nf:

In .\modules\nf-core\bcftools\mpileup\main.nf line 38:

    --fasta-ref $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fasta-ref "$fasta" \

In .\modules\nf-core\bcftools\mpileup\main.nf line 39:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\mpileup\main.nf line 40:

    $bam \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam" \

In .\modules\nf-core\bcftools\mpileup\main.nf line 41:

    $intervals_cmd \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$intervals_cmd" \

In .\modules\nf-core\bcftools\mpileup\main.nf line 42:

    $mpileup \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$mpileup" \

In .\modules\nf-core\bcftools\mpileup\main.nf line 43:

    | bcftools call --output-type v $args2 \
                                    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | bcftools call --output-type v "$args2" \

In .\modules\nf-core\bcftools\mpileup\main.nf line 45:

    | bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3
                                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                   ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | bcftools view --output-file "${prefix}".vcf.gz --output-type z "$args3"

In .\modules\nf-core\bcftools\mpileup\main.nf line 49:

tabix -p vcf -f ${prefix}.vcf.gz
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
tabix -p vcf -f "${prefix}".vcf.gz

In .\modules\nf-core\bcftools\mpileup\main.nf line 51:

bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bcftools stats "${prefix}".vcf.gz > "${prefix}".bcftools_stats.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\norm\main.nf:

In .\modules\nf-core\bcftools\norm\main.nf line 34:

    --fasta-ref ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fasta-ref "${fasta}" \

In .\modules\nf-core\bcftools\norm\main.nf line 35:

    --output ${prefix}.${extension} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}" \

In .\modules\nf-core\bcftools\norm\main.nf line 36:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\norm\main.nf line 37:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\norm\main.nf line 38:

    ${vcf}
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcf}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\pluginimputeinfo\main.nf:

In .\modules\nf-core\bcftools\pluginimputeinfo\main.nf line 37:

    --output ${prefix}.${extension} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}" \

In .\modules\nf-core\bcftools\pluginimputeinfo\main.nf line 38:

    ${regions_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions_file}" \

In .\modules\nf-core\bcftools\pluginimputeinfo\main.nf line 39:

    ${targets_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${targets_file}" \

In .\modules\nf-core\bcftools\pluginimputeinfo\main.nf line 40:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\pluginimputeinfo\main.nf line 41:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\pluginimputeinfo\main.nf line 42:

    ${vcf} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcf}" \

In .\modules\nf-core\bcftools\pluginimputeinfo\main.nf line 44:

    $args2
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\pluginscatter\main.nf:

In .\modules\nf-core\bcftools\pluginscatter\main.nf line 36:

    ${vcf} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcf}" \

In .\modules\nf-core\bcftools\pluginscatter\main.nf line 37:

    ${mandatory_arg} \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${mandatory_arg}" \

In .\modules\nf-core\bcftools\pluginscatter\main.nf line 38:

    ${regions_arg} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions_arg}" \

In .\modules\nf-core\bcftools\pluginscatter\main.nf line 39:

    ${targets_arg} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${targets_arg}" \

In .\modules\nf-core\bcftools\pluginscatter\main.nf line 40:

    --output ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}" \

In .\modules\nf-core\bcftools\pluginscatter\main.nf line 41:

    --prefix ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --prefix "${prefix}" \

In .\modules\nf-core\bcftools\pluginscatter\main.nf line 42:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\bcftools\pluginscatter\main.nf line 43:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

In .\modules\nf-core\bcftools\pluginscatter\main.nf line 45:

mv ${prefix}/* .
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${prefix}"/* .

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\pluginsetgt\main.nf:

In .\modules\nf-core\bcftools\pluginsetgt\main.nf line 39:

    --output ${prefix}.${extension} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}" \

In .\modules\nf-core\bcftools\pluginsetgt\main.nf line 40:

    ${regions_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions_file}" \

In .\modules\nf-core\bcftools\pluginsetgt\main.nf line 41:

    ${targets_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${targets_file}" \

In .\modules\nf-core\bcftools\pluginsetgt\main.nf line 42:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\pluginsetgt\main.nf line 43:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\pluginsetgt\main.nf line 44:

    ${vcf} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcf}" \

In .\modules\nf-core\bcftools\pluginsetgt\main.nf line 46:

    --target-gt ${target_gt} \
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --target-gt "${target_gt}" \

In .\modules\nf-core\bcftools\pluginsetgt\main.nf line 47:

    --new-gt ${new_gt} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --new-gt "${new_gt}" \

In .\modules\nf-core\bcftools\pluginsetgt\main.nf line 48:

    $args2
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\pluginsplit\main.nf:

In .\modules\nf-core\bcftools\pluginsplit\main.nf line 36:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\bcftools\pluginsplit\main.nf line 37:

    ${vcf} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcf}" \

In .\modules\nf-core\bcftools\pluginsplit\main.nf line 38:

    ${samples_arg} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${samples_arg}" \

In .\modules\nf-core\bcftools\pluginsplit\main.nf line 39:

    ${groups_arg} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${groups_arg}" \

In .\modules\nf-core\bcftools\pluginsplit\main.nf line 40:

    ${regions_arg} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions_arg}" \

In .\modules\nf-core\bcftools\pluginsplit\main.nf line 41:

    ${targets_arg} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${targets_arg}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\plugintag2tag\main.nf:

In .\modules\nf-core\bcftools\plugintag2tag\main.nf line 37:

    --output ${prefix}.${extension} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}" \

In .\modules\nf-core\bcftools\plugintag2tag\main.nf line 38:

    ${regions_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions_file}" \

In .\modules\nf-core\bcftools\plugintag2tag\main.nf line 39:

    ${targets_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${targets_file}" \

In .\modules\nf-core\bcftools\plugintag2tag\main.nf line 40:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\plugintag2tag\main.nf line 41:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\plugintag2tag\main.nf line 42:

    ${vcf} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcf}" \

In .\modules\nf-core\bcftools\plugintag2tag\main.nf line 44:

    $args2
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\query\main.nf:

In .\modules\nf-core\bcftools\query\main.nf line 32:

    $regions_file \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$regions_file" \

In .\modules\nf-core\bcftools\query\main.nf line 33:

    $targets_file \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$targets_file" \

In .\modules\nf-core\bcftools\query\main.nf line 34:

    $samples_file \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$samples_file" \

In .\modules\nf-core\bcftools\query\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\query\main.nf line 36:

    $vcf \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf" \

In .\modules\nf-core\bcftools\query\main.nf line 37:

    > ${prefix}.${suffix}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${suffix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\reheader\main.nf:

In .\modules\nf-core\bcftools\reheader\main.nf line 38:

    $fai_argument \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fai_argument" \

In .\modules\nf-core\bcftools\reheader\main.nf line 39:

    $header_argument \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$header_argument" \

In .\modules\nf-core\bcftools\reheader\main.nf line 40:

    $samples_argument \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$samples_argument" \

In .\modules\nf-core\bcftools\reheader\main.nf line 41:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\reheader\main.nf line 42:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\reheader\main.nf line 43:

    $vcf \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf" \

In .\modules\nf-core\bcftools\reheader\main.nf line 45:

    $args2 \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2" \

In .\modules\nf-core\bcftools\reheader\main.nf line 46:

    --output ${prefix}.${extension}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\roh\main.nf:

In .\modules\nf-core\bcftools\roh\main.nf line 36:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\roh\main.nf line 37:

    $af_read \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$af_read" \

In .\modules\nf-core\bcftools\roh\main.nf line 38:

    $gen_map \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gen_map" \

In .\modules\nf-core\bcftools\roh\main.nf line 39:

    $reg_file \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reg_file" \

In .\modules\nf-core\bcftools\roh\main.nf line 40:

    $samp_file \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$samp_file" \

In .\modules\nf-core\bcftools\roh\main.nf line 41:

    $targ_file \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$targ_file" \

In .\modules\nf-core\bcftools\roh\main.nf line 42:

    -o ${prefix}.roh \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".roh \

In .\modules\nf-core\bcftools\roh\main.nf line 43:

    $vcf
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\sort\main.nf:

In .\modules\nf-core\bcftools\sort\main.nf line 34:

    --output ${prefix}.${extension} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}" \

In .\modules\nf-core\bcftools\sort\main.nf line 36:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\sort\main.nf line 37:

    $vcf
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\split\main.nf:

In .\modules\nf-core\bcftools\split\main.nf line 25:

bcftools index -s ${vcf} |\
                  ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bcftools index -s "${vcf}" |\

In .\modules\nf-core\bcftools\split\main.nf line 27:

while read C; do \
      ^--^ SC2162 (info): read without -r will mangle backslashes.
           ^-- SC2034 (warning): C appears unused. Verify use (or export if used externally).

In .\modules\nf-core\bcftools\split\main.nf line 28:

    bcftools view -O z -o ${prefix}.\${C}.vcf.gz ${vcf} --regions "\${C}" ;\
                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                      ^-- SC1083 (warning): This { is literal. Check expression (missing ;/\n?) or quote it.
                                        ^-- SC1083 (warning): This } is literal. Check expression (missing ;/\n?) or quote it.
                                                 ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    bcftools view -O z -o "${prefix}".\${C}.vcf.gz "${vcf}" --regions "\${C}" ;\

For more information:
  https://www.shellcheck.net/wiki/SC1083 -- This { is literal. Check expressi...
  https://www.shellcheck.net/wiki/SC2034 -- C appears unused. Verify use (or ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\stats\main.nf:

In .\modules\nf-core\bcftools\stats\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\stats\main.nf line 36:

    $regions_file \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$regions_file" \

In .\modules\nf-core\bcftools\stats\main.nf line 37:

    $targets_file \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$targets_file" \

In .\modules\nf-core\bcftools\stats\main.nf line 38:

    $samples_file \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$samples_file" \

In .\modules\nf-core\bcftools\stats\main.nf line 39:

    $reference_fasta \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference_fasta" \

In .\modules\nf-core\bcftools\stats\main.nf line 40:

    $exons_file \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$exons_file" \

In .\modules\nf-core\bcftools\stats\main.nf line 41:

    $vcf > ${prefix}.bcftools_stats.txt
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.
           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf" > "${prefix}".bcftools_stats.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcftools\view\main.nf:

In .\modules\nf-core\bcftools\view\main.nf line 38:

    --output ${prefix}.${extension} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${extension}" \

In .\modules\nf-core\bcftools\view\main.nf line 39:

    ${regions_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions_file}" \

In .\modules\nf-core\bcftools\view\main.nf line 40:

    ${targets_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${targets_file}" \

In .\modules\nf-core\bcftools\view\main.nf line 41:

    ${samples_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${samples_file}" \

In .\modules\nf-core\bcftools\view\main.nf line 42:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bcftools\view\main.nf line 43:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bcftools\view\main.nf line 44:

    ${vcf}
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcf}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bcl2fastq\main.nf:

In .\modules\nf-core\bcl2fastq\main.nf line 42:

    if [[ \$(tar -taf ${run_dir} | grep -o -P "^.*?\/" | uniq | wc -l) -eq 1 ]]; then
    ^-- SC1009 (info): The mentioned syntax error was in this if expression.
       ^-- SC1073 (error): Couldn't parse this test expression. Fix to allow more checks.
            ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
            ^-- SC1072 (error): Expected test to end here (don't wrap commands in []/[[]]). Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1072 -- Expected test to end here (don't ...
  https://www.shellcheck.net/wiki/SC1073 -- Couldn't parse this test expressi...

ShellCheck results for .\modules\nf-core\bclconvert\main.nf:

In .\modules\nf-core\bclconvert\main.nf line 42:

    if [[ \$(tar -taf ${run_dir} | grep -o -P "^.*?\/" | uniq | wc -l) -eq 1 ]]; then
    ^-- SC1009 (info): The mentioned syntax error was in this if expression.
       ^-- SC1073 (error): Couldn't parse this test expression. Fix to allow more checks.
            ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
            ^-- SC1072 (error): Expected test to end here (don't wrap commands in []/[[]]). Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1072 -- Expected test to end here (don't ...
  https://www.shellcheck.net/wiki/SC1073 -- Couldn't parse this test expressi...

ShellCheck results for .\modules\nf-core\beagle5\beagle\main.nf:

In .\modules\nf-core\beagle5\beagle\main.nf line 41:

beagle -Xmx${avail_mem}M \
           ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
beagle -Xmx"${avail_mem}"M \

In .\modules\nf-core\beagle5\beagle\main.nf line 42:

    gt=${vcf} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gt="${vcf}" \

In .\modules\nf-core\beagle5\beagle\main.nf line 43:

    out=${prefix} \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    out="${prefix}" \

In .\modules\nf-core\beagle5\beagle\main.nf line 44:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\beagle5\beagle\main.nf line 45:

    ${ref_command} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${ref_command}" \

In .\modules\nf-core\beagle5\beagle\main.nf line 46:

    ${map_command} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${map_command}" \

In .\modules\nf-core\beagle5\beagle\main.nf line 47:

    ${excludesamples_command} \
    ^-----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${excludesamples_command}" \

In .\modules\nf-core\beagle5\beagle\main.nf line 48:

    ${excludemarkers_command} \
    ^-----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${excludemarkers_command}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedgovcf\main.nf:

In .\modules\nf-core\bedgovcf\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedgovcf\main.nf line 28:

    --bed $bed \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bed "$bed" \

In .\modules\nf-core\bedgovcf\main.nf line 29:

    --fai $fai \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fai "$fai" \

In .\modules\nf-core\bedgovcf\main.nf line 30:

    --config $config \
             ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --config "$config" \

In .\modules\nf-core\bedgovcf\main.nf line 31:

    | bgzip --stdout --threads $task.cpus $args2 > ${prefix}.vcf.gz
                               ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                          ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | bgzip --stdout --threads "$task".cpus "$args2" > "${prefix}".vcf.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedops\convert2bed\main.nf:

In .\modules\nf-core\bedops\convert2bed\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedops\convert2bed\main.nf line 27:

    -i $format \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$format" \

In .\modules\nf-core\bedops\convert2bed\main.nf line 28:

    < $in_file \
      ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    < "$in_file" \

In .\modules\nf-core\bedops\convert2bed\main.nf line 29:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedops\gtf2bed\main.nf:

In .\modules\nf-core\bedops\gtf2bed\main.nf line 26:

$gtf \
^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
"$gtf" \

In .\modules\nf-core\bedops\gtf2bed\main.nf line 28:

$args \
^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
"$args" \

In .\modules\nf-core\bedops\gtf2bed\main.nf line 30:

> ${prefix}.bed
  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
> "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\bamtobed\main.nf:

In .\modules\nf-core\bedtools\bamtobed\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\bamtobed\main.nf line 27:

    -i $bam \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bam" \

In .\modules\nf-core\bedtools\bamtobed\main.nf line 28:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\closest\main.nf:

In .\modules\nf-core\bedtools\closest\main.nf line 37:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\bedtools\closest\main.nf line 38:

    -a ${input_1} \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -a "${input_1}" \

In .\modules\nf-core\bedtools\closest\main.nf line 39:

    -b ${input_2} \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "${input_2}" \

In .\modules\nf-core\bedtools\closest\main.nf line 40:

    ${reference} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reference}" \

In .\modules\nf-core\bedtools\closest\main.nf line 41:

    > ${prefix}.${extension}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${extension}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\complement\main.nf:

In .\modules\nf-core\bedtools\complement\main.nf line 28:

    -i $bed \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bed" \

In .\modules\nf-core\bedtools\complement\main.nf line 29:

    -g $sizes \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$sizes" \

In .\modules\nf-core\bedtools\complement\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\complement\main.nf line 31:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\coverage\main.nf:

In .\modules\nf-core\bedtools\coverage\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\coverage\main.nf line 29:

    $reference \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference" \

In .\modules\nf-core\bedtools\coverage\main.nf line 30:

    -a $input_A \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -a "$input_A" \

In .\modules\nf-core\bedtools\coverage\main.nf line 31:

    -b $input_B \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "$input_B" \

In .\modules\nf-core\bedtools\coverage\main.nf line 32:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\genomecov\main.nf:

In .\modules\nf-core\bedtools\genomecov\main.nf line 40:

    -ibam $intervals \
          ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -ibam "$intervals" \

In .\modules\nf-core\bedtools\genomecov\main.nf line 41:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\genomecov\main.nf line 42:

    $sort_cmd \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sort_cmd" \

In .\modules\nf-core\bedtools\genomecov\main.nf line 43:

    > ${prefix}.${extension}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${extension}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\getfasta\main.nf:

In .\modules\nf-core\bedtools\getfasta\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\getfasta\main.nf line 29:

    -fi $fasta \
        ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -fi "$fasta" \

In .\modules\nf-core\bedtools\getfasta\main.nf line 30:

    -bed $bed \
         ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -bed "$bed" \

In .\modules\nf-core\bedtools\getfasta\main.nf line 31:

    -fo ${prefix}.fa
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -fo "${prefix}".fa

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\groupby\main.nf:

In .\modules\nf-core\bedtools\groupby\main.nf line 29:

    -i $bed \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bed" \

In .\modules\nf-core\bedtools\groupby\main.nf line 30:

    ${summary_col} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${summary_col}" \

In .\modules\nf-core\bedtools\groupby\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\groupby\main.nf line 32:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\intersect\main.nf:

In .\modules\nf-core\bedtools\intersect\main.nf line 33:

    -a $intervals1 \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -a "$intervals1" \

In .\modules\nf-core\bedtools\intersect\main.nf line 34:

    -b $intervals2 \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "$intervals2" \

In .\modules\nf-core\bedtools\intersect\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\intersect\main.nf line 36:

    $sizes \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sizes" \

In .\modules\nf-core\bedtools\intersect\main.nf line 37:

    > ${prefix}.${extension}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${extension}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\jaccard\main.nf:

In .\modules\nf-core\bedtools\jaccard\main.nf line 27:

    -a ${input_a} \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -a "${input_a}" \

In .\modules\nf-core\bedtools\jaccard\main.nf line 28:

    -b ${input_b} \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "${input_b}" \

In .\modules\nf-core\bedtools\jaccard\main.nf line 29:

    ${genome} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${genome}" \

In .\modules\nf-core\bedtools\jaccard\main.nf line 30:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\bedtools\jaccard\main.nf line 31:

    > ${prefix}.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\makewindows\main.nf:

In .\modules\nf-core\bedtools\makewindows\main.nf line 28:

    ${arg_input} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${arg_input}" \

In .\modules\nf-core\bedtools\makewindows\main.nf line 29:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\bedtools\makewindows\main.nf line 30:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\map\main.nf:

In .\modules\nf-core\bedtools\map\main.nf line 32:

    -a $intervals1 \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -a "$intervals1" \

In .\modules\nf-core\bedtools\map\main.nf line 33:

    -b $intervals2 \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "$intervals2" \

In .\modules\nf-core\bedtools\map\main.nf line 34:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\map\main.nf line 35:

    $sizes \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sizes" \

In .\modules\nf-core\bedtools\map\main.nf line 36:

    > ${prefix}.${extension}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${extension}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\maskfasta\main.nf:

In .\modules\nf-core\bedtools\maskfasta\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\maskfasta\main.nf line 28:

    -fi $fasta \
        ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -fi "$fasta" \

In .\modules\nf-core\bedtools\maskfasta\main.nf line 29:

    -bed $bed \
         ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -bed "$bed" \

In .\modules\nf-core\bedtools\maskfasta\main.nf line 30:

    -fo ${prefix}.fa
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -fo "${prefix}".fa

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\merge\main.nf:

In .\modules\nf-core\bedtools\merge\main.nf line 27:

    -i $bed \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bed" \

In .\modules\nf-core\bedtools\merge\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\merge\main.nf line 29:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\multiinter\main.nf:

In .\modules\nf-core\bedtools\multiinter\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\multiinter\main.nf line 30:

    $sizes_cmd \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sizes_cmd" \

In .\modules\nf-core\bedtools\multiinter\main.nf line 31:

    -i $beds \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$beds" \

In .\modules\nf-core\bedtools\multiinter\main.nf line 32:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\nuc\main.nf:

In .\modules\nf-core\bedtools\nuc\main.nf line 27:

    -fi ${fasta} \
        ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -fi "${fasta}" \

In .\modules\nf-core\bedtools\nuc\main.nf line 28:

    -bed ${intervals} \
         ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -bed "${intervals}" \

In .\modules\nf-core\bedtools\nuc\main.nf line 29:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\bedtools\nuc\main.nf line 30:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\shift\main.nf:

In .\modules\nf-core\bedtools\shift\main.nf line 28:

    -i $bed \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bed" \

In .\modules\nf-core\bedtools\shift\main.nf line 29:

    -g $chrom_sizes \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$chrom_sizes" \

In .\modules\nf-core\bedtools\shift\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\shift\main.nf line 31:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\shuffle\main.nf:

In .\modules\nf-core\bedtools\shuffle\main.nf line 32:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\shuffle\main.nf line 33:

    -i $intervals \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$intervals" \

In .\modules\nf-core\bedtools\shuffle\main.nf line 34:

    -g $chrom_sizes \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$chrom_sizes" \

In .\modules\nf-core\bedtools\shuffle\main.nf line 35:

    $exclude_arg \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$exclude_arg" \

In .\modules\nf-core\bedtools\shuffle\main.nf line 36:

    $include_arg \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$include_arg" \

In .\modules\nf-core\bedtools\shuffle\main.nf line 37:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\slop\main.nf:

In .\modules\nf-core\bedtools\slop\main.nf line 28:

    -i $bed \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bed" \

In .\modules\nf-core\bedtools\slop\main.nf line 29:

    -g $sizes \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$sizes" \

In .\modules\nf-core\bedtools\slop\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\slop\main.nf line 31:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\sort\main.nf:

In .\modules\nf-core\bedtools\sort\main.nf line 32:

    -i $intervals \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$intervals" \

In .\modules\nf-core\bedtools\sort\main.nf line 33:

    $genome_cmd \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$genome_cmd" \

In .\modules\nf-core\bedtools\sort\main.nf line 34:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\sort\main.nf line 35:

    > ${prefix}.${extension}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${extension}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\split\main.nf:

In .\modules\nf-core\bedtools\split\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\split\main.nf line 28:

    -n ${count} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -n "${count}" \

In .\modules\nf-core\bedtools\split\main.nf line 29:

    -i ${bed} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${bed}" \

In .\modules\nf-core\bedtools\split\main.nf line 30:

    -p ${prefix}
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\subtract\main.nf:

In .\modules\nf-core\bedtools\subtract\main.nf line 29:

    -a $intervals1 \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -a "$intervals1" \

In .\modules\nf-core\bedtools\subtract\main.nf line 30:

    -b $intervals2 \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "$intervals2" \

In .\modules\nf-core\bedtools\subtract\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\subtract\main.nf line 32:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bedtools\unionbedg\main.nf:

In .\modules\nf-core\bedtools\unionbedg\main.nf line 29:

    -i $bedgraph \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bedgraph" \

In .\modules\nf-core\bedtools\unionbedg\main.nf line 30:

    $sizes \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sizes" \

In .\modules\nf-core\bedtools\unionbedg\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bedtools\unionbedg\main.nf line 32:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bioawk\main.nf:

In .\modules\nf-core\bioawk\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bioawk\main.nf line 28:

    $input \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" \

In .\modules\nf-core\bioawk\main.nf line 29:

    > ${prefix}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"

In .\modules\nf-core\bioawk\main.nf line 31:

gzip ${prefix}
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\biobambam\bammarkduplicates2\main.nf:

In .\modules\nf-core\biobambam\bammarkduplicates2\main.nf line 24:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\biobambam\bammarkduplicates2\main.nf line 25:

    I=$bam \
      ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    I="$bam" \

In .\modules\nf-core\biobambam\bammarkduplicates2\main.nf line 26:

    O=${prefix}.bam \
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    O="${prefix}".bam \

In .\modules\nf-core\biobambam\bammarkduplicates2\main.nf line 27:

    M=${prefix}.metrics.txt \
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    M="${prefix}".metrics.txt \

In .\modules\nf-core\biobambam\bammarkduplicates2\main.nf line 28:

    tmpfile=$prefix \
            ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    tmpfile="$prefix" \

In .\modules\nf-core\biobambam\bammarkduplicates2\main.nf line 29:

    markthreads=$task.cpus
                ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    markthreads="$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\biobambam\bammerge\main.nf:

In .\modules\nf-core\biobambam\bammerge\main.nf line 29:

    I=${input_string} \
      ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    I="${input_string}" \

In .\modules\nf-core\biobambam\bammerge\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\biobambam\bammerge\main.nf line 31:

    > ${prefix}.bam
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bam

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\biobambam\bamsormadup\main.nf:

In .\modules\nf-core\biobambam\bamsormadup\main.nf line 32:

    I=${input_string} \
      ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    I="${input_string}" \

In .\modules\nf-core\biobambam\bamsormadup\main.nf line 36:

    $args2 \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2" \

In .\modules\nf-core\biobambam\bamsormadup\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\biobambam\bamsormadup\main.nf line 39:

    M=${prefix}.metrics.txt \
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    M="${prefix}".metrics.txt \

In .\modules\nf-core\biobambam\bamsormadup\main.nf line 40:

    tmpfile=$prefix \
            ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    tmpfile="$prefix" \

In .\modules\nf-core\biobambam\bamsormadup\main.nf line 41:

    threads=$task.cpus \
            ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    threads="$task".cpus \

In .\modules\nf-core\biobambam\bamsormadup\main.nf line 42:

    > ${prefix}.${suffix}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${suffix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\biohansel\main.nf:

In .\modules\nf-core\biohansel\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\biohansel\main.nf line 31:

    $scheme_metadata_opt \
    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$scheme_metadata_opt" \

In .\modules\nf-core\biohansel\main.nf line 32:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\biohansel\main.nf line 33:

    --output-summary ${prefix}-summary.txt \
                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-summary "${prefix}"-summary.txt \

In .\modules\nf-core\biohansel\main.nf line 34:

    --output-kmer-results ${prefix}-kmer-results.txt \
                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-kmer-results "${prefix}"-kmer-results.txt \

In .\modules\nf-core\biohansel\main.nf line 35:

    --output-simple-summary ${prefix}-simple-summary.txt \
                            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-simple-summary "${prefix}"-simple-summary.txt \

In .\modules\nf-core\biohansel\main.nf line 36:

    $input_type \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_type" \

In .\modules\nf-core\biohansel\main.nf line 37:

    $seqs
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$seqs"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\biscuit\align\main.nf:

In .\modules\nf-core\biscuit\align\main.nf line 30:

ln -sf \$(readlink $fasta) $index/$fasta
^-------^ SC2226 (warning): This ln has no destination. Check the arguments, or specify '.' explicitly.
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2226 -- This ln has no destination. Check...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\biscuit\biscuitblaster\main.nf:

In .\modules\nf-core\biscuit\biscuitblaster\main.nf line 31:

ln -sf \$(readlink $fasta) $index/$fasta
^-------^ SC2226 (warning): This ln has no destination. Check the arguments, or specify '.' explicitly.
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2226 -- This ln has no destination. Check...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\biscuit\bsconv\main.nf:

In .\modules\nf-core\biscuit\bsconv\main.nf line 28:

ln -sf \$(readlink $fasta) $index/$fasta
^-------^ SC2226 (warning): This ln has no destination. Check the arguments, or specify '.' explicitly.
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2226 -- This ln has no destination. Check...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\biscuit\epiread\main.nf:

In .\modules\nf-core\biscuit\epiread\main.nf line 38:

ln -sf \$(readlink $fasta) $index/$fasta
^-------^ SC2226 (warning): This ln has no destination. Check the arguments, or specify '.' explicitly.
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2226 -- This ln has no destination. Check...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\biscuit\index\main.nf:

In .\modules\nf-core\biscuit\index\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\biscuit\index\main.nf line 26:

    $fasta
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\biscuit\mergecg\main.nf:

In .\modules\nf-core\biscuit\mergecg\main.nf line 28:

ln -sf \$(readlink $fasta) $index/$fasta
^-------^ SC2226 (warning): This ln has no destination. Check the arguments, or specify '.' explicitly.
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2226 -- This ln has no destination. Check...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\biscuit\pileup\main.nf:

In .\modules\nf-core\biscuit\pileup\main.nf line 32:

ln -sf \$(readlink $fasta) $index/$fasta
^-------^ SC2226 (warning): This ln has no destination. Check the arguments, or specify '.' explicitly.
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2226 -- This ln has no destination. Check...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\biscuit\qc\main.nf:

In .\modules\nf-core\biscuit\qc\main.nf line 27:

ln -sf \$(readlink $fasta) $index/$fasta
^-------^ SC2226 (warning): This ln has no destination. Check the arguments, or specify '.' explicitly.
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2226 -- This ln has no destination. Check...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\biscuit\vcf2bed\main.nf:

In .\modules\nf-core\biscuit\vcf2bed\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\biscuit\vcf2bed\main.nf line 27:

    $vcf \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf" \

In .\modules\nf-core\biscuit\vcf2bed\main.nf line 29:

    | bgzip $args2 -c > ${prefix}.bed.gz
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | bgzip "$args2" -c > "${prefix}".bed.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bismark\align\main.nf:

In .\modules\nf-core\bismark\align\main.nf line 60:

    ${fastq} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fastq}" \

In .\modules\nf-core\bismark\align\main.nf line 61:

    --genome ${index} \
             ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --genome "${index}" \

In .\modules\nf-core\bismark\align\main.nf line 63:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bismark\coverage2cytosine\main.nf:

In .\modules\nf-core\bismark\coverage2cytosine\main.nf line 29:

    ${coverage_file} \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${coverage_file}" \

In .\modules\nf-core\bismark\coverage2cytosine\main.nf line 30:

    --genome ${index} \
             ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --genome "${index}" \

In .\modules\nf-core\bismark\coverage2cytosine\main.nf line 31:

    --output ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}" \

In .\modules\nf-core\bismark\coverage2cytosine\main.nf line 33:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bismark\deduplicate\main.nf:

In .\modules\nf-core\bismark\deduplicate\main.nf line 27:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\bismark\deduplicate\main.nf line 28:

    ${seqtype} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${seqtype}" \

In .\modules\nf-core\bismark\deduplicate\main.nf line 29:

    --bam ${bam}
          ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bam "${bam}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bismark\genomepreparation\main.nf:

In .\modules\nf-core\bismark\genomepreparation\main.nf line 24:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bismark\methylationextractor\main.nf:

In .\modules\nf-core\bismark\methylationextractor\main.nf line 39:

    ${bam} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bam}" \

In .\modules\nf-core\bismark\methylationextractor\main.nf line 44:

    ${seqtype} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${seqtype}" \

In .\modules\nf-core\bismark\methylationextractor\main.nf line 45:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bismark\report\main.nf:

In .\modules\nf-core\bismark\report\main.nf line 23:

bismark2report ${args}
               ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bismark2report "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bismark\summary\main.nf:

In .\modules\nf-core\bismark\summary\main.nf line 26:

bismark2summary ${bam.join(' ')}
                ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bismark2summary "${bam.join(' ')}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\blast\blastdbcmd\main.nf:

In .\modules\nf-core\blast\blastdbcmd\main.nf line 34:

DB=`find -L ./ -name "*.nhr" | sed 's/\.nhr\$//'`
   ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
DB=$(find -L ./ -name "*.nhr" | sed 's/\.nhr\$//')

In .\modules\nf-core\blast\blastdbcmd\main.nf line 37:

    DB=`find -L ./ -name "*.phr" | sed 's/\.phr\$//'`
    ^-- SC2034 (warning): DB appears unused. Verify use (or export if used externally).
       ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
    DB=$(find -L ./ -name "*.phr" | sed 's/\.phr\$//')

In .\modules\nf-core\blast\blastdbcmd\main.nf line 42:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\blast\blastdbcmd\main.nf line 43:

    -out ${prefix}.${extension} \
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                   ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -out "${prefix}"."${extension}" \

In .\modules\nf-core\blast\blastdbcmd\main.nf line 44:

    ${input}
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input}"

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- DB appears unused. Verify use (or...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\blast\blastn\main.nf:

In .\modules\nf-core\blast\blastn\main.nf line 29:

    gzip -c -d ${fasta} > ${fasta_name}
               ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "${fasta}" > "${fasta_name}"

In .\modules\nf-core\blast\blastn\main.nf line 32:

DB=`find -L ./ -name "*.nal" | sed 's/\.nal\$//'`
   ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
DB=$(find -L ./ -name "*.nal" | sed 's/\.nal\$//')

In .\modules\nf-core\blast\blastn\main.nf line 33:

if [ -z "\$DB" ]; then
         ^--^ SC2157 (error): Argument to -z is always false due to literal strings.

In .\modules\nf-core\blast\blastn\main.nf line 34:

    DB=`find -L ./ -name "*.nin" | sed 's/\.nin\$//'`
    ^-- SC2034 (warning): DB appears unused. Verify use (or export if used externally).
       ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
    DB=$(find -L ./ -name "*.nin" | sed 's/\.nin\$//')

In .\modules\nf-core\blast\blastn\main.nf line 39:

    -num_threads ${task.cpus} \
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -num_threads "${task.cpus}" \

In .\modules\nf-core\blast\blastn\main.nf line 41:

    -query ${fasta_name} \
           ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -query "${fasta_name}" \

In .\modules\nf-core\blast\blastn\main.nf line 42:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\blast\blastn\main.nf line 43:

    -out ${prefix}.txt
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -out "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2157 -- Argument to -z is always false du...
  https://www.shellcheck.net/wiki/SC2034 -- DB appears unused. Verify use (or...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\blast\blastp\main.nf:

In .\modules\nf-core\blast\blastp\main.nf line 42:

    gzip -c -d ${fasta} > ${fasta_name}
               ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "${fasta}" > "${fasta_name}"

In .\modules\nf-core\blast\blastp\main.nf line 45:

DB=`find -L ./ -name "*.phr" | sed 's/\.phr\$//'`
^-- SC2034 (warning): DB appears unused. Verify use (or export if used externally).
   ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
DB=$(find -L ./ -name "*.phr" | sed 's/\.phr\$//')

In .\modules\nf-core\blast\blastp\main.nf line 47:

    -query ${fasta_name} \
           ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -query "${fasta_name}" \

In .\modules\nf-core\blast\blastp\main.nf line 48:

    -out ${prefix}.${out_ext} \
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                   ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -out "${prefix}"."${out_ext}" \

In .\modules\nf-core\blast\blastp\main.nf line 50:

    -num_threads ${task.cpus} \
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -num_threads "${task.cpus}" \

In .\modules\nf-core\blast\blastp\main.nf line 51:

    -outfmt ${outfmt} \
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -outfmt "${outfmt}" \

In .\modules\nf-core\blast\blastp\main.nf line 52:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- DB appears unused. Verify use (or...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\blast\makeblastdb\main.nf:

In .\modules\nf-core\blast\makeblastdb\main.nf line 27:

    gzip -c -d ${fasta} > ${fasta_name}
               ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "${fasta}" > "${fasta_name}"

In .\modules\nf-core\blast\makeblastdb\main.nf line 31:

    -in ${fasta_name} \
        ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -in "${fasta_name}" \

In .\modules\nf-core\blast\makeblastdb\main.nf line 32:

    -out ${prefix}/${fasta_name} \
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                   ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -out "${prefix}"/"${fasta_name}" \

In .\modules\nf-core\blast\makeblastdb\main.nf line 33:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\blast\tblastn\main.nf:

In .\modules\nf-core\blast\tblastn\main.nf line 28:

    gzip -c -d ${fasta} > ${fasta_name}
               ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "${fasta}" > "${fasta_name}"

In .\modules\nf-core\blast\tblastn\main.nf line 31:

DB=`find -L ./ -name "*.nal" | sed 's/\.nal\$//'`
   ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
DB=$(find -L ./ -name "*.nal" | sed 's/\.nal\$//')

In .\modules\nf-core\blast\tblastn\main.nf line 32:

if [ -z "\$DB" ]; then
         ^--^ SC2157 (error): Argument to -z is always false due to literal strings.

In .\modules\nf-core\blast\tblastn\main.nf line 33:

    DB=`find -L ./ -name "*.nin" | sed 's/\.nin\$//'`
    ^-- SC2034 (warning): DB appears unused. Verify use (or export if used externally).
       ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
    DB=$(find -L ./ -name "*.nin" | sed 's/\.nin\$//')

In .\modules\nf-core\blast\tblastn\main.nf line 38:

    -num_threads ${task.cpus} \
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -num_threads "${task.cpus}" \

In .\modules\nf-core\blast\tblastn\main.nf line 40:

    -query ${fasta_name} \
           ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -query "${fasta_name}" \

In .\modules\nf-core\blast\tblastn\main.nf line 41:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\blast\tblastn\main.nf line 42:

    -out ${prefix}.txt
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -out "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2157 -- Argument to -z is always false du...
  https://www.shellcheck.net/wiki/SC2034 -- DB appears unused. Verify use (or...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\blast\updateblastdb\main.nf:

In .\modules\nf-core\blast\updateblastdb\main.nf line 24:

mkdir ${prefix}; cd ${prefix}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                 ^----------^ SC2164 (warning): Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mkdir "${prefix}"; cd "${prefix}" || exit

In .\modules\nf-core\blast\updateblastdb\main.nf line 27:

    ${name} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${name}" \

In .\modules\nf-core\blast\updateblastdb\main.nf line 28:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

In .\modules\nf-core\blast\updateblastdb\main.nf line 30:

cd ..
^---^ SC2103 (info): Use a ( subshell ) to avoid having to cd back.

For more information:
  https://www.shellcheck.net/wiki/SC2164 -- Use 'cd ... || exit' or 'cd ... |...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2103 -- Use a ( subshell ) to avoid havin...

ShellCheck results for .\modules\nf-core\blat\main.nf:

In .\modules\nf-core\blat\main.nf line 30:

    gunzip -cdf $query > ${prefix}.fasta
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gunzip -cdf "$query" > "${prefix}".fasta

In .\modules\nf-core\blat\main.nf line 31:

    in=${prefix}.fasta
    ^-- SC2034 (warning): in appears unused. Verify use (or export if used externally).

In .\modules\nf-core\blat\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\blat\main.nf line 36:

    $subject \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$subject" \

In .\modules\nf-core\blat\main.nf line 38:

    ${prefix}.psl
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".psl

In .\modules\nf-core\blat\main.nf line 42:

    rm ${prefix}.fasta
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    rm "${prefix}".fasta

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- in appears unused. Verify use (or...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bowtie\align\main.nf:

In .\modules\nf-core\bowtie\align\main.nf line 31:

INDEX=\$(find -L ./ -name "*.3.ebwt" | sed 's/\.3.ebwt\$//')
^---^ SC2034 (warning): INDEX appears unused. Verify use (or export if used externally).
        ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
        ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- INDEX appears unused. Verify use ...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\bowtie\build\main.nf:

In .\modules\nf-core\bowtie\build\main.nf line 24:

bowtie-build --threads $task.cpus $fasta bowtie/${prefix}
                       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                  ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bowtie-build --threads "$task".cpus "$fasta" bowtie/"${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bowtie2\align\main.nf:

In .\modules\nf-core\bowtie2\align\main.nf line 53:

INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\.rev.1.bt2\$//"`
      ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
INDEX=$(find -L ./ -name "*.rev.1.bt2" | sed "s/\.rev.1.bt2\$//")

In .\modules\nf-core\bowtie2\align\main.nf line 54:

[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\.rev.1.bt2l\$//"`
      ^-----^ SC2157 (error): Argument to -z is always false due to literal strings.
                    ^---^ SC2034 (warning): INDEX appears unused. Verify use (or export if used externally).
                          ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
[ -z "\$INDEX" ] && INDEX=$(find -L ./ -name "*.rev.1.bt2l" | sed "s/\.rev.1.bt2l\$//")

In .\modules\nf-core\bowtie2\align\main.nf line 55:

[ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
      ^-----^ SC2157 (error): Argument to -z is always false due to literal strings.

In .\modules\nf-core\bowtie2\align\main.nf line 59:

    $reads_args \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads_args" \

In .\modules\nf-core\bowtie2\align\main.nf line 60:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\bowtie2\align\main.nf line 61:

    $unaligned \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$unaligned" \

In .\modules\nf-core\bowtie2\align\main.nf line 62:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bowtie2\align\main.nf line 63:

    2> >(tee ${prefix}.bowtie2.log >&2) \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    2> >(tee "${prefix}".bowtie2.log >&2) \

In .\modules\nf-core\bowtie2\align\main.nf line 64:

    | samtools $samtools_command $args2 --threads $task.cpus ${reference} -o ${prefix}.${extension} -
               ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                  ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                             ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | samtools "$samtools_command" "$args2" --threads "$task".cpus "${reference}" -o "${prefix}"."${extension}" -

In .\modules\nf-core\bowtie2\align\main.nf line 66:

if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
if [ -f "${prefix}".unmapped.fastq.1.gz ]; then

In .\modules\nf-core\bowtie2\align\main.nf line 67:

    mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    mv "${prefix}".unmapped.fastq.1.gz "${prefix}".unmapped_1.fastq.gz

In .\modules\nf-core\bowtie2\align\main.nf line 70:

if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
if [ -f "${prefix}".unmapped.fastq.2.gz ]; then

In .\modules\nf-core\bowtie2\align\main.nf line 71:

    mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    mv "${prefix}".unmapped.fastq.2.gz "${prefix}".unmapped_2.fastq.gz

For more information:
  https://www.shellcheck.net/wiki/SC2157 -- Argument to -z is always false du...
  https://www.shellcheck.net/wiki/SC2034 -- INDEX appears unused. Verify use ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bowtie2\build\main.nf:

In .\modules\nf-core\bowtie2\build\main.nf line 24:

bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                         ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                        ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bowtie2-build "$args" --threads "$task".cpus "$fasta" bowtie2/"${fasta.baseName}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bracken\bracken\main.nf:

In .\modules\nf-core\bracken\bracken\main.nf line 29:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\bracken\bracken\main.nf line 30:

    -d '${database}' \
       ^-----------^ SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\bracken\bracken\main.nf line 31:

    -i '${kraken_report}' \
       ^----------------^ SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\bracken\bracken\main.nf line 32:

    -o '${bracken_report}' \
       ^-----------------^ SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\bracken\bracken\main.nf line 33:

    -w '${bracken_kraken_style_report}'
       ^-- SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

For more information:
  https://www.shellcheck.net/wiki/SC2016 -- Expressions don't expand in singl...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bracken\build\main.nf:

In .\modules\nf-core\bracken\build\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bracken\build\main.nf line 26:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\bracken\build\main.nf line 27:

    -d $kraken2db
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -d "$kraken2db"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bracken\combinebrackenoutputs\main.nf:

In .\modules\nf-core\bracken\combinebrackenoutputs\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bracken\combinebrackenoutputs\main.nf line 28:

    --files ${input} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --files "${input}" \

In .\modules\nf-core\bracken\combinebrackenoutputs\main.nf line 29:

    -o ${prefix}.txt
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\busco\busco\main.nf:

In .\modules\nf-core\busco\busco\main.nf line 65:

if [ ! -w "\${AUGUSTUS_CONFIG_PATH}" ]; then
^-- SC1046 (error): Couldn't find 'fi' for this 'if'.
^-- SC1073 (error): Couldn't parse this if expression. Fix to allow more checks.

In .\modules\nf-core\busco\busco\main.nf line 67:

    AUG_CONF_DIR=\$( mktemp -d -p \$PWD )
                   ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
                   ^-- SC1047 (error): Expected 'fi' matching previously mentioned 'if'.
                   ^-- SC1072 (error): Expected 'fi'. Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1046 -- Couldn't find 'fi' for this 'if'.
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1047 -- Expected 'fi' matching previously...

ShellCheck results for .\modules\nf-core\busco\download\main.nf:

In .\modules\nf-core\busco\download\main.nf line 25:

    --download $lineage \
               ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --download "$lineage" \

In .\modules\nf-core\busco\download\main.nf line 26:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\busco\generateplot\main.nf:

In .\modules\nf-core\busco\generateplot\main.nf line 24:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\busco\generateplot\main.nf line 27:

mv ./busco/busco_figure.png ${prefix}.png
                            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv ./busco/busco_figure.png "${prefix}".png

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\busco\phylogenomics\main.nf:

In .\modules\nf-core\busco\phylogenomics\main.nf line 27:

    -i ${busco} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${busco}" \

In .\modules\nf-core\busco\phylogenomics\main.nf line 28:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\busco\phylogenomics\main.nf line 29:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\busco\phylogenomics\main.nf line 30:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bwa\aln\main.nf:

In .\modules\nf-core\bwa\aln\main.nf line 27:

INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb\$//'`
^---^ SC2034 (warning): INDEX appears unused. Verify use (or export if used externally).
      ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
INDEX=$(find -L ./ -name "*.amb" | sed 's/\.amb\$//')

In .\modules\nf-core\bwa\aln\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bwa\aln\main.nf line 31:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\bwa\aln\main.nf line 32:

    -f ${prefix}.sai \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -f "${prefix}".sai \

In .\modules\nf-core\bwa\aln\main.nf line 34:

    ${reads}
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reads}"

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- INDEX appears unused. Verify use ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\bwa\index\main.nf:

In .\modules\nf-core\bwa\index\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bwa\index\main.nf line 30:

    -p bwa/${prefix} \
           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p bwa/"${prefix}" \

In .\modules\nf-core\bwa\index\main.nf line 31:

    $fasta
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bwa\mem\main.nf:

In .\modules\nf-core\bwa\mem\main.nf line 39:

INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb\$//'`
^---^ SC2034 (warning): INDEX appears unused. Verify use (or export if used externally).
      ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
INDEX=$(find -L ./ -name "*.amb" | sed 's/\.amb\$//')

In .\modules\nf-core\bwa\mem\main.nf line 42:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bwa\mem\main.nf line 43:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\bwa\mem\main.nf line 45:

    $reads \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads" \

In .\modules\nf-core\bwa\mem\main.nf line 46:

    | samtools $samtools_command $args2 ${reference} --threads $task.cpus -o ${prefix}.${extension} -
               ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                               ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | samtools "$samtools_command" "$args2" "${reference}" --threads "$task".cpus -o "${prefix}"."${extension}" -

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- INDEX appears unused. Verify use ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\bwa\sampe\main.nf:

In .\modules\nf-core\bwa\sampe\main.nf line 27:

INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb\$//'`
^---^ SC2034 (warning): INDEX appears unused. Verify use (or export if used externally).
      ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
INDEX=$(find -L ./ -name "*.amb" | sed 's/\.amb\$//')

In .\modules\nf-core\bwa\sampe\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bwa\sampe\main.nf line 31:

    $read_group \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$read_group" \

In .\modules\nf-core\bwa\sampe\main.nf line 33:

    $sai \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sai" \

In .\modules\nf-core\bwa\sampe\main.nf line 34:

    $reads | samtools sort -@ ${task.cpus} -O bam - > ${prefix}.bam
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads" | samtools sort -@ "${task.cpus}" -O bam - > "${prefix}".bam

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- INDEX appears unused. Verify use ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\bwa\samse\main.nf:

In .\modules\nf-core\bwa\samse\main.nf line 27:

INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb\$//'`
^---^ SC2034 (warning): INDEX appears unused. Verify use (or export if used externally).
      ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
INDEX=$(find -L ./ -name "*.amb" | sed 's/\.amb\$//')

In .\modules\nf-core\bwa\samse\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bwa\samse\main.nf line 31:

    $read_group \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$read_group" \

In .\modules\nf-core\bwa\samse\main.nf line 33:

    $sai \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sai" \

In .\modules\nf-core\bwa\samse\main.nf line 34:

    $reads | samtools sort -@ ${task.cpus - 1} -O bam - > ${prefix}.bam
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                              ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads" | samtools sort -@ "${task.cpus - 1}" -O bam - > "${prefix}".bam

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- INDEX appears unused. Verify use ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\bwamem2\index\main.nf:

In .\modules\nf-core\bwamem2\index\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bwamem2\index\main.nf line 30:

    $fasta -p bwamem2/${prefix}
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" -p bwamem2/"${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bwamem2\mem\main.nf:

In .\modules\nf-core\bwamem2\mem\main.nf line 40:

INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb\$//'`
^---^ SC2034 (warning): INDEX appears unused. Verify use (or export if used externally).
      ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
INDEX=$(find -L ./ -name "*.amb" | sed 's/\.amb\$//')

In .\modules\nf-core\bwamem2\mem\main.nf line 44:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bwamem2\mem\main.nf line 45:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\bwamem2\mem\main.nf line 47:

    $reads \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads" \

In .\modules\nf-core\bwamem2\mem\main.nf line 48:

    | samtools $samtools_command $args2 -@ $task.cpus ${reference} -o ${prefix}.${extension} -
               ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                           ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                      ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | samtools "$samtools_command" "$args2" -@ "$task".cpus "${reference}" -o "${prefix}"."${extension}" -

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- INDEX appears unused. Verify use ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\bwameme\index\main.nf:

In .\modules\nf-core\bwameme\index\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bwameme\index\main.nf line 29:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\bwameme\index\main.nf line 30:

    -p bwameme/$prefix \
               ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p bwameme/"$prefix" \

In .\modules\nf-core\bwameme\index\main.nf line 31:

    $fasta
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta"

In .\modules\nf-core\bwameme\index\main.nf line 33:

build_rmis_dna.sh bwameme/$prefix
                          ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
build_rmis_dna.sh bwameme/"$prefix"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\bwameme\mem\main.nf:

In .\modules\nf-core\bwameme\mem\main.nf line 55:

INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb\$//'`
^---^ SC2034 (warning): INDEX appears unused. Verify use (or export if used externally).
      ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
INDEX=$(find -L ./ -name "*.amb" | sed 's/\.amb\$//')

In .\modules\nf-core\bwameme\mem\main.nf line 59:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\bwameme\mem\main.nf line 60:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\bwameme\mem\main.nf line 62:

    $reads \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads" \

In .\modules\nf-core\bwameme\mem\main.nf line 63:

    $mbuffer_command \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$mbuffer_command" \

In .\modules\nf-core\bwameme\mem\main.nf line 64:

    | samtools $samtools_command $args2 $mem_per_thread -@ $threads ${reference} -o ${prefix}.${extension} -
               ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                        ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                           ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | samtools "$samtools_command" "$args2" "$mem_per_thread" -@ "$threads" "${reference}" -o "${prefix}"."${extension}" -

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- INDEX appears unused. Verify use ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\bwameth\align\main.nf:

In .\modules\nf-core\bwameth\align\main.nf line 30:

touch -c $index/*
         ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch -c "$index"/*

In .\modules\nf-core\bwameth\align\main.nf line 32:

ln -sf \$(readlink $fasta) $index/$fasta
^-------^ SC2226 (warning): This ln has no destination. Check the arguments, or specify '.' explicitly.
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2226 -- This ln has no destination. Check...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...

ShellCheck results for .\modules\nf-core\bwameth\index\main.nf:

In .\modules\nf-core\bwameth\index\main.nf line 24:

bwameth.py index $fasta
                 ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bwameth.py index "$fasta"

In .\modules\nf-core\bwameth\index\main.nf line 26:

rm $fasta
   ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
rm "$fasta"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cadd\main.nf:

In .\modules\nf-core\cadd\main.nf line 42:

    -o ${prefix}.tsv.gz \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".tsv.gz \

In .\modules\nf-core\cadd\main.nf line 43:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\cadd\main.nf line 44:

    ${vcf}
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcf}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cafe\main.nf:

In .\modules\nf-core\cafe\main.nf line 29:

tr '\r' '\n' < $infile > infile.txt
               ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
tr '\r' '\n' < "$infile" > infile.txt

In .\modules\nf-core\cafe\main.nf line 30:

tr '\r' '\n' < $tree > treefile.txt
               ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
tr '\r' '\n' < "$tree" > treefile.txt

In .\modules\nf-core\cafe\main.nf line 34:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cafe\main.nf line 35:

    --cores ${task.cpus} \
            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cores "${task.cpus}" \

In .\modules\nf-core\cafe\main.nf line 36:

    -o ${prefix}
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\calder2\main.nf:

In .\modules\nf-core\calder2\main.nf line 32:

binsize="\$(cooler info --field bin-size $cool$suffix)"
^-----^ SC2034 (warning): binsize appears unused. Verify use (or export if used externally).

In .\modules\nf-core\calder2\main.nf line 34:

calder --input $cool$suffix \
               ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
calder --input "$cool""$suffix" \

In .\modules\nf-core\calder2\main.nf line 35:

    --outpath ${prefix} \
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outpath "${prefix}" \

In .\modules\nf-core\calder2\main.nf line 36:

    --nproc $cpus \
            ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nproc "$cpus" \

In .\modules\nf-core\calder2\main.nf line 39:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- binsize appears unused. Verify us...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\canu\main.nf:

In .\modules\nf-core\canu\main.nf line 36:

    -p ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${prefix}" \

In .\modules\nf-core\canu\main.nf line 37:

    genomeSize=${genomesize} \
               ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    genomeSize="${genomesize}" \

In .\modules\nf-core\canu\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\canu\main.nf line 39:

    maxThreads=$task.cpus \
               ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    maxThreads="$task".cpus \

In .\modules\nf-core\canu\main.nf line 40:

    $mode $reads
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
          ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$mode" "$reads"

In .\modules\nf-core\canu\main.nf line 42:

gzip *.fasta
     ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cat\cat\main.nf:

In .\modules\nf-core\cat\cat\main.nf line 46:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cat\cat\main.nf line 47:

    ${file_list.join(' ')} \
    ^--------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${file_list.join(' ')}" \

In .\modules\nf-core\cat\cat\main.nf line 48:

    $command2 \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$command2" \

In .\modules\nf-core\cat\cat\main.nf line 49:

    > ${prefix}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cat\fastq\main.nf:

In .\modules\nf-core\cat\fastq\main.nf line 26:

cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
    ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
cat "${readList.join(' ')}" > "${prefix}".merged.fastq.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\catpack\addnames\main.nf:

In .\modules\nf-core\catpack\addnames\main.nf line 29:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\catpack\addnames\main.nf line 30:

    -i ${input} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${input}" \

In .\modules\nf-core\catpack\addnames\main.nf line 31:

    -t ${taxonomy} \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "${taxonomy}" \

In .\modules\nf-core\catpack\addnames\main.nf line 32:

    -o ${prefix}.txt
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\catpack\bins\main.nf:

In .\modules\nf-core\catpack\bins\main.nf line 36:

    -n ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -n "${task.cpus}" \

In .\modules\nf-core\catpack\bins\main.nf line 38:

    -d ${database} \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -d "${database}" \

In .\modules\nf-core\catpack\bins\main.nf line 39:

    -t ${taxonomy} \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "${taxonomy}" \

In .\modules\nf-core\catpack\bins\main.nf line 40:

    ${premade_proteins} \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${premade_proteins}" \

In .\modules\nf-core\catpack\bins\main.nf line 41:

    ${premade_table} \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${premade_table}" \

In .\modules\nf-core\catpack\bins\main.nf line 42:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\catpack\bins\main.nf line 43:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\catpack\contigs\main.nf:

In .\modules\nf-core\catpack\contigs\main.nf line 36:

    --nproc ${task.cpus} \
            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nproc "${task.cpus}" \

In .\modules\nf-core\catpack\contigs\main.nf line 37:

    --contigs_fasta ${contigs} \
                    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --contigs_fasta "${contigs}" \

In .\modules\nf-core\catpack\contigs\main.nf line 38:

    --database_folder ${database} \
                      ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --database_folder "${database}" \

In .\modules\nf-core\catpack\contigs\main.nf line 39:

    --taxonomy_folder ${taxonomy} \
                      ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --taxonomy_folder "${taxonomy}" \

In .\modules\nf-core\catpack\contigs\main.nf line 40:

    --out_prefix ${prefix} \
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --out_prefix "${prefix}" \

In .\modules\nf-core\catpack\contigs\main.nf line 41:

    ${premade_proteins} \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${premade_proteins}" \

In .\modules\nf-core\catpack\contigs\main.nf line 42:

    ${premade_table} \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${premade_table}" \

In .\modules\nf-core\catpack\contigs\main.nf line 43:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\catpack\download\main.nf:

In .\modules\nf-core\catpack\download\main.nf line 26:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\catpack\download\main.nf line 27:

    --db ${db}
         ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --db "${db}"

In .\modules\nf-core\catpack\download\main.nf line 28:

    -o ${prefix}/
    ^-- SC2215 (warning): This flag is used as a command name. Bad line break or missing [ .. ]?
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}"/

For more information:
  https://www.shellcheck.net/wiki/SC2215 -- This flag is used as a command na...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\catpack\prepare\main.nf:

In .\modules\nf-core\catpack\prepare\main.nf line 29:

    -n ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -n "${task.cpus}" \

In .\modules\nf-core\catpack\prepare\main.nf line 30:

    --db_fasta ${db_fasta} \
               ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --db_fasta "${db_fasta}" \

In .\modules\nf-core\catpack\prepare\main.nf line 31:

    --names ${names} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --names "${names}" \

In .\modules\nf-core\catpack\prepare\main.nf line 32:

    --nodes ${nodes} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nodes "${nodes}" \

In .\modules\nf-core\catpack\prepare\main.nf line 33:

    --acc2tax ${acc2tax} \
              ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --acc2tax "${acc2tax}" \

In .\modules\nf-core\catpack\prepare\main.nf line 34:

    --db_dir ${prefix}/ \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --db_dir "${prefix}"/ \

In .\modules\nf-core\catpack\prepare\main.nf line 35:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\catpack\reads\main.nf:

In .\modules\nf-core\catpack\reads\main.nf line 59:

    ${insert_reads} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_reads}" \

In .\modules\nf-core\catpack\reads\main.nf line 60:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\catpack\reads\main.nf line 61:

    -d ${database} \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -d "${database}" \

In .\modules\nf-core\catpack\reads\main.nf line 62:

    -c ${contigs} \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -c "${contigs}" \

In .\modules\nf-core\catpack\reads\main.nf line 63:

    -t ${taxonomy} \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "${taxonomy}" \

In .\modules\nf-core\catpack\reads\main.nf line 64:

    -m ${mode} \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -m "${mode}" \

In .\modules\nf-core\catpack\reads\main.nf line 65:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\catpack\reads\main.nf line 66:

    ${insert_bins} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_bins}" \

In .\modules\nf-core\catpack\reads\main.nf line 67:

    ${insert_bam_aligned} \
    ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_bam_aligned}" \

In .\modules\nf-core\catpack\reads\main.nf line 68:

    ${insert_bam_unaligned} \
    ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_bam_unaligned}" \

In .\modules\nf-core\catpack\reads\main.nf line 69:

    ${insert_c2c} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_c2c}" \

In .\modules\nf-core\catpack\reads\main.nf line 70:

    ${insert_b2c} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_b2c}" \

In .\modules\nf-core\catpack\reads\main.nf line 71:

    ${insert_u2c} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_u2c}" \

In .\modules\nf-core\catpack\reads\main.nf line 72:

    ${insert_proteins} \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_proteins}" \

In .\modules\nf-core\catpack\reads\main.nf line 73:

    ${insert_diamond_alignment}
    ^-------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_diamond_alignment}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\catpack\summarise\main.nf:

In .\modules\nf-core\catpack\summarise\main.nf line 30:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\catpack\summarise\main.nf line 31:

    -i ${classification} \
       ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${classification}" \

In .\modules\nf-core\catpack\summarise\main.nf line 32:

    ${insert_contigs} \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_contigs}" \

In .\modules\nf-core\catpack\summarise\main.nf line 33:

    -o ${prefix}.txt
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cdhit\cdhit\main.nf:

In .\modules\nf-core\cdhit\cdhit\main.nf line 32:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cdhit\cdhit\main.nf line 33:

    -i $sequences \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$sequences" \

In .\modules\nf-core\cdhit\cdhit\main.nf line 34:

    -o ${prefix}.fasta \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".fasta \

In .\modules\nf-core\cdhit\cdhit\main.nf line 35:

    -M $avail_mem \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -M "$avail_mem" \

In .\modules\nf-core\cdhit\cdhit\main.nf line 36:

    -T $task.cpus
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -T "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cdhit\cdhitest\main.nf:

In .\modules\nf-core\cdhit\cdhitest\main.nf line 34:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cdhit\cdhitest\main.nf line 35:

    -i ${sequences} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${sequences}" \

In .\modules\nf-core\cdhit\cdhitest\main.nf line 36:

    -o ${meta.id}.${suffix} \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${meta.id}"."${suffix}" \

In .\modules\nf-core\cdhit\cdhitest\main.nf line 37:

    -M $avail_mem \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -M "$avail_mem" \

In .\modules\nf-core\cdhit\cdhitest\main.nf line 38:

    -T $task.cpus
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -T "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\celesta\main.nf:

In .\modules\nf-core\celesta\main.nf line 32:

    -i $img_data \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$img_data" \

In .\modules\nf-core\celesta\main.nf line 33:

    -s $signature \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -s "$signature" \

In .\modules\nf-core\celesta\main.nf line 34:

    --high $high_thresholds \
           ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --high "$high_thresholds" \

In .\modules\nf-core\celesta\main.nf line 35:

    $low_thresholds_cmd \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$low_thresholds_cmd" \

In .\modules\nf-core\celesta\main.nf line 37:

    -t $prefix \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$prefix" \

In .\modules\nf-core\celesta\main.nf line 38:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellbender\removebackground\main.nf:

In .\modules\nf-core\cellbender\removebackground\main.nf line 36:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\cellbender\removebackground\main.nf line 37:

    --cpu-threads ${task.cpus} \
                  ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpu-threads "${task.cpus}" \

In .\modules\nf-core\cellbender\removebackground\main.nf line 38:

    ${use_gpu} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${use_gpu}" \

In .\modules\nf-core\cellbender\removebackground\main.nf line 39:

    --input ${h5ad} \
            ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${h5ad}" \

In .\modules\nf-core\cellbender\removebackground\main.nf line 40:

    --output ${prefix}.h5
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".h5

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellpose\main.nf:

In .\modules\nf-core\cellpose\main.nf line 31:

    --image_path $image \
                 ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --image_path "$image" \

In .\modules\nf-core\cellpose\main.nf line 33:

    $model_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$model_command" \

In .\modules\nf-core\cellpose\main.nf line 34:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellranger\count\main.nf:

In .\modules\nf-core\cellranger\count\main.nf line 35:

echo "$prefix" > ${prefix}/outs/fake_file.txt
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "$prefix" > "${prefix}"/outs/fake_file.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellranger\mkfastq\main.nf:

In .\modules\nf-core\cellranger\mkfastq\main.nf line 31:

    --id=${prefix}_outs \
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --id="${prefix}"_outs \

In .\modules\nf-core\cellranger\mkfastq\main.nf line 32:

    --run=$bcl \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --run="$bcl" \

In .\modules\nf-core\cellranger\mkfastq\main.nf line 33:

    --csv=$csv \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --csv="$csv" \

In .\modules\nf-core\cellranger\mkfastq\main.nf line 34:

    --localcores=${task.cpus} \
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --localcores="${task.cpus}" \

In .\modules\nf-core\cellranger\mkfastq\main.nf line 35:

    --localmem=${task.memory.toGiga()} \
               ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --localmem="${task.memory.toGiga()}" \

In .\modules\nf-core\cellranger\mkfastq\main.nf line 36:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellranger\mkgtf\main.nf:

In .\modules\nf-core\cellranger\mkgtf\main.nf line 27:

    $gtf \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gtf" \

In .\modules\nf-core\cellranger\mkgtf\main.nf line 28:

    ${prefix}.gtf \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".gtf \

In .\modules\nf-core\cellranger\mkgtf\main.nf line 29:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellranger\mkref\main.nf:

In .\modules\nf-core\cellranger\mkref\main.nf line 31:

    --genome=$reference_name \
             ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --genome="$reference_name" \

In .\modules\nf-core\cellranger\mkref\main.nf line 32:

    --fasta=$fasta \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fasta="$fasta" \

In .\modules\nf-core\cellranger\mkref\main.nf line 33:

    --genes=$gtf \
            ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --genes="$gtf" \

In .\modules\nf-core\cellranger\mkref\main.nf line 34:

    --localcores=${task.cpus} \
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --localcores="${task.cpus}" \

In .\modules\nf-core\cellranger\mkref\main.nf line 35:

    --localmem=${task.memory.toGiga()} \
               ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --localmem="${task.memory.toGiga()}" \

In .\modules\nf-core\cellranger\mkref\main.nf line 36:

    --nthreads=${task.cpus} \
               ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nthreads="${task.cpus}" \

In .\modules\nf-core\cellranger\mkref\main.nf line 37:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellranger\mkvdjref\main.nf:

In .\modules\nf-core\cellranger\mkvdjref\main.nf line 33:

    --genome=$reference_name \
             ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --genome="$reference_name" \

In .\modules\nf-core\cellranger\mkvdjref\main.nf line 34:

    ${gtf_in} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${gtf_in}" \

In .\modules\nf-core\cellranger\mkvdjref\main.nf line 35:

    ${fasta_in} \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fasta_in}" \

In .\modules\nf-core\cellranger\mkvdjref\main.nf line 36:

    ${seqs_in} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${seqs_in}" \

In .\modules\nf-core\cellranger\mkvdjref\main.nf line 37:

    --localcores=${task.cpus} \
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --localcores="${task.cpus}" \

In .\modules\nf-core\cellranger\mkvdjref\main.nf line 38:

    --localmem=${task.memory.toGiga()} \
               ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --localmem="${task.memory.toGiga()}" \

In .\modules\nf-core\cellranger\mkvdjref\main.nf line 39:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellranger\multi\main.nf:

In .\modules\nf-core\cellranger\multi\main.nf line 139:

touch ${prefix}/outs/fake_file.txt
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}"/outs/fake_file.txt

In .\modules\nf-core\cellranger\multi\main.nf line 140:

echo -n "" >> ${prefix}/outs/fake_file.txt
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo -n "" >> "${prefix}"/outs/fake_file.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellranger\vdj\main.nf:

In .\modules\nf-core\cellranger\vdj\main.nf line 29:

    --id='${prefix}' \
         ^---------^ SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\cellranger\vdj\main.nf line 31:

    --reference=$reference_name \
                ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference="$reference_name" \

In .\modules\nf-core\cellranger\vdj\main.nf line 32:

    --localcores=${task.cpus} \
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --localcores="${task.cpus}" \

In .\modules\nf-core\cellranger\vdj\main.nf line 33:

    --localmem=${task.memory.toGiga()} \
               ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --localmem="${task.memory.toGiga()}" \

In .\modules\nf-core\cellranger\vdj\main.nf line 34:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2016 -- Expressions don't expand in singl...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellrangerarc\count\main.nf:

In .\modules\nf-core\cellrangerarc\count\main.nf line 32:

fastq_folder=\$(readlink -f fastqs)
^----------^ SC2034 (warning): fastq_folder appears unused. Verify use (or export if used externally).
               ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
               ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- fastq_folder appears unused. Veri...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\cellrangerarc\mkfastq\main.nf:

In .\modules\nf-core\cellrangerarc\mkfastq\main.nf line 25:

cellranger-arc mkfastq --id=${bcl.getSimpleName()} \
                            ^--------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
cellranger-arc mkfastq --id="${bcl.getSimpleName()}" \

In .\modules\nf-core\cellrangerarc\mkfastq\main.nf line 26:

    --run=$bcl \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --run="$bcl" \

In .\modules\nf-core\cellrangerarc\mkfastq\main.nf line 27:

    --csv=$csv \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --csv="$csv" \

In .\modules\nf-core\cellrangerarc\mkfastq\main.nf line 28:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellrangerarc\mkgtf\main.nf:

In .\modules\nf-core\cellrangerarc\mkgtf\main.nf line 27:

    $gtf \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gtf" \

In .\modules\nf-core\cellrangerarc\mkgtf\main.nf line 28:

    ${gtf.baseName}.filtered.gtf \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${gtf.baseName}".filtered.gtf \

In .\modules\nf-core\cellrangerarc\mkgtf\main.nf line 29:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellrangerarc\mkref\main.nf:

In .\modules\nf-core\cellrangerarc\mkref\main.nf line 76:

    --nthreads=${task.cpus} \
               ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nthreads="${task.cpus}" \

In .\modules\nf-core\cellrangerarc\mkref\main.nf line 77:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellrangeratac\count\main.nf:

In .\modules\nf-core\cellrangeratac\count\main.nf line 30:

    --id='${meta.id}' \
         ^----------^ SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\cellrangeratac\count\main.nf line 32:

    --reference=$reference_name \
                ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference="$reference_name" \

In .\modules\nf-core\cellrangeratac\count\main.nf line 33:

    --sample=$sample_arg \
             ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --sample="$sample_arg" \

In .\modules\nf-core\cellrangeratac\count\main.nf line 34:

    --localcores=$task.cpus \
                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --localcores="$task".cpus \

In .\modules\nf-core\cellrangeratac\count\main.nf line 35:

    --localmem=${task.memory.toGiga()} \
               ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --localmem="${task.memory.toGiga()}" \

In .\modules\nf-core\cellrangeratac\count\main.nf line 36:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2016 -- Expressions don't expand in singl...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellrangeratac\mkfastq\main.nf:

In .\modules\nf-core\cellrangeratac\mkfastq\main.nf line 26:

cellranger-atac mkfastq --id=${bcl.getSimpleName()} \
                             ^--------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
cellranger-atac mkfastq --id="${bcl.getSimpleName()}" \

In .\modules\nf-core\cellrangeratac\mkfastq\main.nf line 27:

    --run=$bcl \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --run="$bcl" \

In .\modules\nf-core\cellrangeratac\mkfastq\main.nf line 28:

    --csv=$csv \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --csv="$csv" \

In .\modules\nf-core\cellrangeratac\mkfastq\main.nf line 29:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellrangeratac\mkref\main.nf:

In .\modules\nf-core\cellrangeratac\mkref\main.nf line 30:

    --config=$reference_config \
             ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --config="$reference_config" \

In .\modules\nf-core\cellrangeratac\mkref\main.nf line 31:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cellsnp\modea\main.nf:

In .\modules\nf-core\cellsnp\modea\main.nf line 30:

cellsnp-lite -s $bam \
                ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
cellsnp-lite -s "$bam" \

In .\modules\nf-core\cellsnp\modea\main.nf line 31:

    -b $barcode \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "$barcode" \

In .\modules\nf-core\cellsnp\modea\main.nf line 32:

    $region_file \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$region_file" \

In .\modules\nf-core\cellsnp\modea\main.nf line 35:

    --nproc $task.cpus \
            ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nproc "$task".cpus \

In .\modules\nf-core\cellsnp\modea\main.nf line 36:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

In .\modules\nf-core\cellsnp\modea\main.nf line 38:

mv cellSNP.base.vcf.gz ${prefix}.base.vcf.gz
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv cellSNP.base.vcf.gz "${prefix}".base.vcf.gz

In .\modules\nf-core\cellsnp\modea\main.nf line 40:

    mv cellSNP.cells.vcf.gz ${prefix}.cells.vcf.gz
                            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    mv cellSNP.cells.vcf.gz "${prefix}".cells.vcf.gz

In .\modules\nf-core\cellsnp\modea\main.nf line 42:

mv cellSNP.tag.AD.mtx ${prefix}.tag.AD.mtx
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv cellSNP.tag.AD.mtx "${prefix}".tag.AD.mtx

In .\modules\nf-core\cellsnp\modea\main.nf line 43:

mv cellSNP.tag.DP.mtx ${prefix}.tag.DP.mtx
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv cellSNP.tag.DP.mtx "${prefix}".tag.DP.mtx

In .\modules\nf-core\cellsnp\modea\main.nf line 44:

mv cellSNP.tag.OTH.mtx ${prefix}.tag.OTH.mtx
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv cellSNP.tag.OTH.mtx "${prefix}".tag.OTH.mtx

In .\modules\nf-core\cellsnp\modea\main.nf line 45:

mv cellSNP.samples.tsv ${prefix}.samples.tsv
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv cellSNP.samples.tsv "${prefix}".samples.tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\centrifuge\build\main.nf:

In .\modules\nf-core\centrifuge\build\main.nf line 29:

mkdir ${prefix}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mkdir "${prefix}"

In .\modules\nf-core\centrifuge\build\main.nf line 32:

    -p ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${task.cpus}" \

In .\modules\nf-core\centrifuge\build\main.nf line 33:

    ${fasta} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fasta}" \

In .\modules\nf-core\centrifuge\build\main.nf line 34:

    ${prefix}/${prefix} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"/"${prefix}" \

In .\modules\nf-core\centrifuge\build\main.nf line 35:

    --conversion-table ${conversion_table} \
                       ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --conversion-table "${conversion_table}" \

In .\modules\nf-core\centrifuge\build\main.nf line 36:

    --taxonomy-tree ${taxonomy_tree} \
                    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --taxonomy-tree "${taxonomy_tree}" \

In .\modules\nf-core\centrifuge\build\main.nf line 37:

    --name-table ${name_table} \
                 ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --name-table "${name_table}" \

In .\modules\nf-core\centrifuge\build\main.nf line 38:

    ${size_table_cmd} \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${size_table_cmd}" \

In .\modules\nf-core\centrifuge\build\main.nf line 39:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\centrifuge\centrifuge\main.nf:

In .\modules\nf-core\centrifuge\centrifuge\main.nf line 43:

db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/\.1.cf\$//'`
^-----^ SC2034 (warning): db_name appears unused. Verify use (or export if used externally).
        ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.
                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
db_name=$(find -L "${db}" -name "*.1.cf" -not -name "._*"  | sed 's/\.1.cf\$//')

In .\modules\nf-core\centrifuge\centrifuge\main.nf line 53:

    -p ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${task.cpus}" \

In .\modules\nf-core\centrifuge\centrifuge\main.nf line 54:

    ${paired} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${paired}" \

In .\modules\nf-core\centrifuge\centrifuge\main.nf line 55:

    --report-file ${prefix}.report.txt \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --report-file "${prefix}".report.txt \

In .\modules\nf-core\centrifuge\centrifuge\main.nf line 56:

    -S ${prefix}.results.txt \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -S "${prefix}".results.txt \

In .\modules\nf-core\centrifuge\centrifuge\main.nf line 57:

    ${unaligned} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${unaligned}" \

In .\modules\nf-core\centrifuge\centrifuge\main.nf line 58:

    ${aligned} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${aligned}" \

In .\modules\nf-core\centrifuge\centrifuge\main.nf line 59:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- db_name appears unused. Verify us...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\centrifuge\kreport\main.nf:

In .\modules\nf-core\centrifuge\kreport\main.nf line 25:

db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/\.1.cf\$//'`
^-----^ SC2034 (warning): db_name appears unused. Verify use (or export if used externally).
        ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.
                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
db_name=$(find -L "${db}" -name "*.1.cf" -not -name "._*"  | sed 's/\.1.cf\$//')

In .\modules\nf-core\centrifuge\kreport\main.nf line 27:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\centrifuge\kreport\main.nf line 29:

    ${report} > ${prefix}.txt
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${report}" > "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- db_name appears unused. Verify us...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\checkm\lineagewf\main.nf:

In .\modules\nf-core\checkm\lineagewf\main.nf line 33:

    -t ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "${task.cpus}" \

In .\modules\nf-core\checkm\lineagewf\main.nf line 34:

    -f ${prefix}.tsv \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -f "${prefix}".tsv \

In .\modules\nf-core\checkm\lineagewf\main.nf line 36:

    --pplacer_threads ${task.cpus} \
                      ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --pplacer_threads "${task.cpus}" \

In .\modules\nf-core\checkm\lineagewf\main.nf line 37:

    -x ${fasta_ext} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -x "${fasta_ext}" \

In .\modules\nf-core\checkm\lineagewf\main.nf line 38:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\checkm\lineagewf\main.nf line 40:

    ${prefix}
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\checkm\qa\main.nf:

In .\modules\nf-core\checkm\qa\main.nf line 31:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\checkm\qa\main.nf line 32:

    --file ${prefix}.${suffix} \
           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --file "${prefix}"."${suffix}" \

In .\modules\nf-core\checkm\qa\main.nf line 33:

    ${marker_file} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${marker_file}" \

In .\modules\nf-core\checkm\qa\main.nf line 34:

    ${analysis_dir} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${analysis_dir}" \

In .\modules\nf-core\checkm\qa\main.nf line 35:

    ${coverage} \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${coverage}" \

In .\modules\nf-core\checkm\qa\main.nf line 36:

    ${exclude} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${exclude}" \

In .\modules\nf-core\checkm\qa\main.nf line 37:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\checkm2\databasedownload\main.nf:

In .\modules\nf-core\checkm2\databasedownload\main.nf line 30:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\checkm2\databasedownload\main.nf line 31:

    --checksum ${checksum} \
               ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --checksum "${checksum}" \

In .\modules\nf-core\checkm2\databasedownload\main.nf line 32:

    https://zenodo.org/records/${zenodo_id}/files/checkm2_database.tar.gz
                               ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    https://zenodo.org/records/"${zenodo_id}"/files/checkm2_database.tar.gz

In .\modules\nf-core\checkm2\databasedownload\main.nf line 35:

db_path=\$(find -name *.dmnd)
^-----^ SC2034 (warning): db_path appears unused. Verify use (or export if used externally).
          ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
          ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- db_path appears unused. Verify us...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...

ShellCheck results for .\modules\nf-core\checkm2\predict\main.nf:

In .\modules\nf-core\checkm2\predict\main.nf line 28:

    --input ${fasta} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${fasta}" \

In .\modules\nf-core\checkm2\predict\main.nf line 29:

    --output-directory ${prefix} \
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-directory "${prefix}" \

In .\modules\nf-core\checkm2\predict\main.nf line 30:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\checkm2\predict\main.nf line 31:

    --database_path ${db} \
                    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --database_path "${db}" \

In .\modules\nf-core\checkm2\predict\main.nf line 32:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

In .\modules\nf-core\checkm2\predict\main.nf line 34:

cp ${prefix}/quality_report.tsv ${prefix}_checkm2_report.tsv
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
cp "${prefix}"/quality_report.tsv "${prefix}"_checkm2_report.tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\checkqc\main.nf:

In .\modules\nf-core\checkqc\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\checkqc\main.nf line 30:

    $config \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$config" \

In .\modules\nf-core\checkqc\main.nf line 32:

    $run_dir > checkqc_report.json || true
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$run_dir" > checkqc_report.json || true

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\checkv\downloaddatabase\main.nf:

In .\modules\nf-core\checkv\downloaddatabase\main.nf line 22:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\checkv\downloaddatabase\main.nf line 23:

    ./$prefix/
      ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    ./"$prefix"/

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\checkv\endtoend\main.nf:

In .\modules\nf-core\checkv\endtoend\main.nf line 33:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\checkv\endtoend\main.nf line 34:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\checkv\endtoend\main.nf line 35:

    -d $db \
       ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -d "$db" \

In .\modules\nf-core\checkv\endtoend\main.nf line 36:

    $fasta \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" \

In .\modules\nf-core\checkv\endtoend\main.nf line 37:

    $prefix
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$prefix"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\checkv\updatedatabase\main.nf:

In .\modules\nf-core\checkv\updatedatabase\main.nf line 27:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\checkv\updatedatabase\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\checkv\updatedatabase\main.nf line 29:

    $checkv_db \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$checkv_db" \

In .\modules\nf-core\checkv\updatedatabase\main.nf line 30:

    ./$prefix/  \
      ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    ./"$prefix"/  \

In .\modules\nf-core\checkv\updatedatabase\main.nf line 31:

    $update_sequence \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$update_sequence" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\chewbbaca\allelecall\main.nf:

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 36:

    --cpu ${task.cpus} \
          ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpu "${task.cpus}" \

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 37:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 39:

    --schema-directory ${scheme} \
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --schema-directory "${scheme}" \

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 42:

mv results/results_statistics.tsv ${prefix}_results_statistics.tsv
                                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv results/results_statistics.tsv "${prefix}"_results_statistics.tsv

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 43:

mv results/results_contigsInfo.tsv ${prefix}_results_contigsInfo.tsv
                                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv results/results_contigsInfo.tsv "${prefix}"_results_contigsInfo.tsv

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 44:

mv results/results_alleles.tsv ${prefix}_results_alleles.tsv
                               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv results/results_alleles.tsv "${prefix}"_results_alleles.tsv

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 45:

mv results/logging_info.txt ${prefix}_logging_info.txt
                            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv results/logging_info.txt "${prefix}"_logging_info.txt

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 48:

[ -f results/paralogous_counts.tsv ] && mv results/paralogous_counts.tsv ${prefix}_paralogous_counts.tsv
                                                                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
[ -f results/paralogous_counts.tsv ] && mv results/paralogous_counts.tsv "${prefix}"_paralogous_counts.tsv

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 49:

[ -f results/paralogous_loci.tsv ] && mv results/paralogous_loci.tsv ${prefix}_paralogous_loci.tsv
                                                                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
[ -f results/paralogous_loci.tsv ] && mv results/paralogous_loci.tsv "${prefix}"_paralogous_loci.tsv

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 50:

[ -f results/cds_coordinates.tsv ] && mv results/cds_coordinates.tsv ${prefix}_cds_coordinates.tsv
                                                                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
[ -f results/cds_coordinates.tsv ] && mv results/cds_coordinates.tsv "${prefix}"_cds_coordinates.tsv

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 51:

[ -f results/invalid_cds.txt ] && mv results/invalid_cds.txt ${prefix}_invalid_cds.txt
                                                             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
[ -f results/invalid_cds.txt ] && mv results/invalid_cds.txt "${prefix}"_invalid_cds.txt

In .\modules\nf-core\chewbbaca\allelecall\main.nf line 52:

[ -f results/loci_summary_stats.tsv ] && mv results/loci_summary_stats.tsv ${prefix}_loci_summary_stats.tsv
                                                                           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
[ -f results/loci_summary_stats.tsv ] && mv results/loci_summary_stats.tsv "${prefix}"_loci_summary_stats.tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\chewbbaca\createschema\main.nf:

In .\modules\nf-core\chewbbaca\createschema\main.nf line 38:

    $schema \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$schema" \

In .\modules\nf-core\chewbbaca\createschema\main.nf line 39:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\chewbbaca\createschema\main.nf line 40:

    $prodigal_tf \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$prodigal_tf" \

In .\modules\nf-core\chewbbaca\createschema\main.nf line 41:

    $cds \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$cds" \

In .\modules\nf-core\chewbbaca\createschema\main.nf line 42:

    --cpu $task.cpus
          ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpu "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\chopper\main.nf:

In .\modules\nf-core\chopper\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\chopper\main.nf line 32:

    $fastq | \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fastq" | \

In .\modules\nf-core\chopper\main.nf line 34:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\chopper\main.nf line 35:

    $fasta_filtering \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta_filtering" \

In .\modules\nf-core\chopper\main.nf line 36:

    $args2 | \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2" | \

In .\modules\nf-core\chopper\main.nf line 38:

    $args3 > ${prefix}.fastq.gz
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args3" > "${prefix}".fastq.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\chromap\chromap\main.nf:

In .\modules\nf-core\chromap\chromap\main.nf line 56:

}
^-- SC1089 (error): Parsing stopped here. Is this keyword correctly matched up?

For more information:
  https://www.shellcheck.net/wiki/SC1089 -- Parsing stopped here. Is this key...

ShellCheck results for .\modules\nf-core\chromap\index\main.nf:

In .\modules\nf-core\chromap\index\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\chromap\index\main.nf line 27:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\chromap\index\main.nf line 28:

    -r $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -r "$fasta" \

In .\modules\nf-core\chromap\index\main.nf line 29:

    -o ${prefix}.index
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".index

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\chromograph\main.nf:

In .\modules\nf-core\chromograph\main.nf line 53:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\chromograph\main.nf line 54:

    $autozyg_param \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$autozyg_param" \

In .\modules\nf-core\chromograph\main.nf line 55:

    $coverage_param \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$coverage_param" \

In .\modules\nf-core\chromograph\main.nf line 56:

    $exome_param \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$exome_param" \

In .\modules\nf-core\chromograph\main.nf line 57:

    $fracsnp_param \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fracsnp_param" \

In .\modules\nf-core\chromograph\main.nf line 58:

    $ideogram_param \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ideogram_param" \

In .\modules\nf-core\chromograph\main.nf line 59:

    $regions_param \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$regions_param" \

In .\modules\nf-core\chromograph\main.nf line 60:

    $sites_param \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sites_param" \

In .\modules\nf-core\chromograph\main.nf line 61:

    --outd ${prefix}
           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outd "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\circexplorer2\annotate\main.nf:

In .\modules\nf-core\circexplorer2\annotate\main.nf line 28:

    -r $gene_annotation \
       ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -r "$gene_annotation" \

In .\modules\nf-core\circexplorer2\annotate\main.nf line 29:

    -g $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$fasta" \

In .\modules\nf-core\circexplorer2\annotate\main.nf line 30:

    -b $junctions \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "$junctions" \

In .\modules\nf-core\circexplorer2\annotate\main.nf line 31:

    -o ${prefix}.txt \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".txt \

In .\modules\nf-core\circexplorer2\annotate\main.nf line 32:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\circexplorer2\parse\main.nf:

In .\modules\nf-core\circexplorer2\parse\main.nf line 28:

    $aligner \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$aligner" \

In .\modules\nf-core\circexplorer2\parse\main.nf line 29:

    $fusions \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fusions" \

In .\modules\nf-core\circexplorer2\parse\main.nf line 30:

    -b ${prefix}.bed \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "${prefix}".bed \

In .\modules\nf-core\circexplorer2\parse\main.nf line 31:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\circularmapper\circulargenerator\main.nf:

In .\modules\nf-core\circularmapper\circulargenerator\main.nf line 32:

    -e ${elongation_factor} \
       ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -e "${elongation_factor}" \

In .\modules\nf-core\circularmapper\circulargenerator\main.nf line 33:

    -i ${reference} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${reference}" \

In .\modules\nf-core\circularmapper\circulargenerator\main.nf line 34:

    -s ${target} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -s "${target}" \

In .\modules\nf-core\circularmapper\circulargenerator\main.nf line 35:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

In .\modules\nf-core\circularmapper\circulargenerator\main.nf line 39:

    mv ${reference.getSimpleName()}_${elongation_factor}${full_extension} ${prefix}_${elongation_factor}.fasta
       ^--------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                        ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    mv "${reference.getSimpleName()}"_"${elongation_factor}""${full_extension}" "${prefix}"_"${elongation_factor}".fasta

In .\modules\nf-core\circularmapper\circulargenerator\main.nf line 40:

    mv ${reference}_${elongation_factor}_elongated ${prefix}.fasta_${elongation_factor}_elongated
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                   ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    mv "${reference}"_"${elongation_factor}"_elongated "${prefix}".fasta_"${elongation_factor}"_elongated

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\circularmapper\realignsamfile\main.nf:

In .\modules\nf-core\circularmapper\realignsamfile\main.nf line 31:

    -Xmx${task.memory.toGiga()}g \
        ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${task.memory.toGiga()}"g \

In .\modules\nf-core\circularmapper\realignsamfile\main.nf line 32:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\circularmapper\realignsamfile\main.nf line 33:

    -e ${elongation_factor} \
       ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -e "${elongation_factor}" \

In .\modules\nf-core\circularmapper\realignsamfile\main.nf line 34:

    -i ${bam} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${bam}" \

In .\modules\nf-core\circularmapper\realignsamfile\main.nf line 35:

    -r ${fasta}
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -r "${fasta}"

In .\modules\nf-core\circularmapper\realignsamfile\main.nf line 39:

    mv ${bam.getBaseName()}_realigned.bam ${prefix}_realigned.bam
       ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    mv "${bam.getBaseName()}"_realigned.bam "${prefix}"_realigned.bam

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\clair3\main.nf:

In .\modules\nf-core\clair3\main.nf line 45:

    --bam_fn=$bam \
             ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bam_fn="$bam" \

In .\modules\nf-core\clair3\main.nf line 46:

    --ref_fn=$reference \
             ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ref_fn="$reference" \

In .\modules\nf-core\clair3\main.nf line 47:

    --threads=$task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads="$task".cpus \

In .\modules\nf-core\clair3\main.nf line 49:

    --platform=$platform \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --platform="$platform" \

In .\modules\nf-core\clair3\main.nf line 50:

    --model=$model \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --model="$model" \

In .\modules\nf-core\clair3\main.nf line 51:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\clame\main.nf:

In .\modules\nf-core\clame\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\clame\main.nf line 31:

    -nt $task.cpus \
        ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -nt "$task".cpus \

In .\modules\nf-core\clame\main.nf line 32:

    -multiFasta ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -multiFasta "${fasta}" \

In .\modules\nf-core\clame\main.nf line 33:

    -output ${prefix} || test -f ${prefix}.binning
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -output "${prefix}" || test -f "${prefix}".binning

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\clipkit\main.nf:

In .\modules\nf-core\clipkit\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\clipkit\main.nf line 29:

    $aln \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$aln" \

In .\modules\nf-core\clipkit\main.nf line 30:

    -o ${prefix}.${out_extension} > ${prefix}.log
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                 ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}"."${out_extension}" > "${prefix}".log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\clippy\main.nf:

In .\modules\nf-core\clippy\main.nf line 28:

clippy -i $bed \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
clippy -i "$bed" \

In .\modules\nf-core\clippy\main.nf line 29:

    -o $prefix \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "$prefix" \

In .\modules\nf-core\clippy\main.nf line 30:

    -a $gtf \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -a "$gtf" \

In .\modules\nf-core\clippy\main.nf line 31:

    -g $fai \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$fai" \

In .\modules\nf-core\clippy\main.nf line 32:

    -t ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "${task.cpus}" \

In .\modules\nf-core\clippy\main.nf line 33:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\clonalframeml\main.nf:

In .\modules\nf-core\clonalframeml\main.nf line 30:

    $newick \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$newick" \

In .\modules\nf-core\clonalframeml\main.nf line 31:

    <(gzip -cdf $msa) \
                ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    <(gzip -cdf "$msa") \

In .\modules\nf-core\clonalframeml\main.nf line 32:

    $prefix \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$prefix" \

In .\modules\nf-core\clonalframeml\main.nf line 33:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\clustalo\align\main.nf:

In .\modules\nf-core\clustalo\align\main.nf line 42:

    -i ${fasta} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${fasta}" \

In .\modules\nf-core\clustalo\align\main.nf line 43:

    $options_tree \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$options_tree" \

In .\modules\nf-core\clustalo\align\main.nf line 44:

    ${fhmm_in} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fhmm_in}" \

In .\modules\nf-core\clustalo\align\main.nf line 45:

    ${fhmm_batch} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fhmm_batch}" \

In .\modules\nf-core\clustalo\align\main.nf line 46:

    ${fprofile1} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fprofile1}" \

In .\modules\nf-core\clustalo\align\main.nf line 47:

    ${fprofile2} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fprofile2}" \

In .\modules\nf-core\clustalo\align\main.nf line 48:

    --threads=${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads="${task.cpus}" \

In .\modules\nf-core\clustalo\align\main.nf line 49:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\clustalo\align\main.nf line 50:

    $write_output
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$write_output"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\clustalo\guidetree\main.nf:

In .\modules\nf-core\clustalo\guidetree\main.nf line 25:

    -i ${fasta} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${fasta}" \

In .\modules\nf-core\clustalo\guidetree\main.nf line 26:

    --guidetree-out ${prefix}.dnd \
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --guidetree-out "${prefix}".dnd \

In .\modules\nf-core\clustalo\guidetree\main.nf line 27:

    --threads=${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads="${task.cpus}" \

In .\modules\nf-core\clustalo\guidetree\main.nf line 28:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cmseq\polymut\main.nf:

In .\modules\nf-core\cmseq\polymut\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cmseq\polymut\main.nf line 30:

    $sortindex \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sortindex" \

In .\modules\nf-core\cmseq\polymut\main.nf line 31:

    $fasta_refid \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta_refid" \

In .\modules\nf-core\cmseq\polymut\main.nf line 32:

    --gff_file $gff \
               ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gff_file "$gff" \

In .\modules\nf-core\cmseq\polymut\main.nf line 33:

    $bam > ${prefix}.txt
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.
           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam" > "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvkit\access\main.nf:

In .\modules\nf-core\cnvkit\access\main.nf line 28:

    $fasta \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" \

In .\modules\nf-core\cnvkit\access\main.nf line 29:

    $exclude_cmd \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$exclude_cmd" \

In .\modules\nf-core\cnvkit\access\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cnvkit\access\main.nf line 31:

    --output ${prefix}.bed
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvkit\antitarget\main.nf:

In .\modules\nf-core\cnvkit\antitarget\main.nf line 27:

    $targets \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$targets" \

In .\modules\nf-core\cnvkit\antitarget\main.nf line 28:

    --output ${prefix}.antitarget.bed \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".antitarget.bed \

In .\modules\nf-core\cnvkit\antitarget\main.nf line 29:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvkit\batch\main.nf:

In .\modules\nf-core\cnvkit\batch\main.nf line 97:

    $tumor_out \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$tumor_out" \

In .\modules\nf-core\cnvkit\batch\main.nf line 98:

    $normal_args \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$normal_args" \

In .\modules\nf-core\cnvkit\batch\main.nf line 99:

    $fasta_args \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta_args" \

In .\modules\nf-core\cnvkit\batch\main.nf line 100:

    $reference_args \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference_args" \

In .\modules\nf-core\cnvkit\batch\main.nf line 101:

    $target_args \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$target_args" \

In .\modules\nf-core\cnvkit\batch\main.nf line 102:

    --processes $task.cpus \
                ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --processes "$task".cpus \

In .\modules\nf-core\cnvkit\batch\main.nf line 103:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvkit\call\main.nf:

In .\modules\nf-core\cnvkit\call\main.nf line 26:

    $cns \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$cns" \

In .\modules\nf-core\cnvkit\call\main.nf line 27:

    $vcf_cmd \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf_cmd" \

In .\modules\nf-core\cnvkit\call\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cnvkit\call\main.nf line 29:

    -o ${prefix}.cns
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".cns

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvkit\export\main.nf:

In .\modules\nf-core\cnvkit\export\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cnvkit\export\main.nf line 27:

    $cns \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$cns" \

In .\modules\nf-core\cnvkit\export\main.nf line 28:

    -o ${prefix}.${suffix}
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}"."${suffix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvkit\genemetrics\main.nf:

In .\modules\nf-core\cnvkit\genemetrics\main.nf line 29:

    $cnr \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$cnr" \

In .\modules\nf-core\cnvkit\genemetrics\main.nf line 30:

    $segments \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$segments" \

In .\modules\nf-core\cnvkit\genemetrics\main.nf line 31:

    --output ${prefix}.tsv \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".tsv \

In .\modules\nf-core\cnvkit\genemetrics\main.nf line 32:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvkit\reference\main.nf:

In .\modules\nf-core\cnvkit\reference\main.nf line 29:

    --fasta $fasta \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fasta "$fasta" \

In .\modules\nf-core\cnvkit\reference\main.nf line 30:

    --targets $targets \
              ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --targets "$targets" \

In .\modules\nf-core\cnvkit\reference\main.nf line 31:

    --antitargets $antitargets \
                  ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --antitargets "$antitargets" \

In .\modules\nf-core\cnvkit\reference\main.nf line 32:

    --output ${prefix}.reference.cnn \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".reference.cnn \

In .\modules\nf-core\cnvkit\reference\main.nf line 33:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvkit\target\main.nf:

In .\modules\nf-core\cnvkit\target\main.nf line 28:

    $baits \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$baits" \

In .\modules\nf-core\cnvkit\target\main.nf line 29:

    $annotate_cmd \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$annotate_cmd" \

In .\modules\nf-core\cnvkit\target\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cnvkit\target\main.nf line 31:

    --output ${prefix}.bed
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvnator\cnvnator\main.nf:

In .\modules\nf-core\cnvnator\cnvnator\main.nf line 37:

    -root ${prefix}.root \
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -root "${prefix}".root \

In .\modules\nf-core\cnvnator\cnvnator\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cnvnator\cnvnator\main.nf line 39:

    $reference \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference" \

In .\modules\nf-core\cnvnator\cnvnator\main.nf line 40:

    $input_cmd \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_cmd" \

In .\modules\nf-core\cnvnator\cnvnator\main.nf line 41:

    $calls_cmd
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$calls_cmd"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvnator\convert2vcf\main.nf:

In .\modules\nf-core\cnvnator\convert2vcf\main.nf line 25:

    ${calls} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${calls}" \

In .\modules\nf-core\cnvnator\convert2vcf\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cnvnator\convert2vcf\main.nf line 27:

    > ${prefix}.vcf
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".vcf

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvpytor\callcnvs\main.nf:

In .\modules\nf-core\cnvpytor\callcnvs\main.nf line 25:

    -root $pytor \
          ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -root "$pytor" \

In .\modules\nf-core\cnvpytor\callcnvs\main.nf line 26:

    $bin_sizes
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bin_sizes"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvpytor\histogram\main.nf:

In .\modules\nf-core\cnvpytor\histogram\main.nf line 26:

    -root $pytor \
          ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -root "$pytor" \

In .\modules\nf-core\cnvpytor\histogram\main.nf line 27:

    -his $bins
         ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -his "$bins"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvpytor\importreaddepth\main.nf:

In .\modules\nf-core\cnvpytor\importreaddepth\main.nf line 28:

    -root ${prefix}.pytor \
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -root "${prefix}".pytor \

In .\modules\nf-core\cnvpytor\importreaddepth\main.nf line 29:

    -rd $input_file \
        ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -rd "$input_file" \

In .\modules\nf-core\cnvpytor\importreaddepth\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cnvpytor\importreaddepth\main.nf line 31:

    $reference
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cnvpytor\partition\main.nf:

In .\modules\nf-core\cnvpytor\partition\main.nf line 25:

    -root $pytor \
          ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -root "$pytor" \

In .\modules\nf-core\cnvpytor\partition\main.nf line 26:

    -partition $bins
               ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -partition "$bins"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cobrameta\main.nf:

In .\modules\nf-core\cobrameta\main.nf line 38:

    --fasta ${fasta} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fasta "${fasta}" \

In .\modules\nf-core\cobrameta\main.nf line 39:

    --coverage ${coverage} \
               ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --coverage "${coverage}" \

In .\modules\nf-core\cobrameta\main.nf line 40:

    --query ${query} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --query "${query}" \

In .\modules\nf-core\cobrameta\main.nf line 41:

    --mapping ${bam} \
              ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --mapping "${bam}" \

In .\modules\nf-core\cobrameta\main.nf line 42:

    --assembler ${assembler} \
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --assembler "${assembler}" \

In .\modules\nf-core\cobrameta\main.nf line 43:

    --mink ${mink} \
           ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --mink "${mink}" \

In .\modules\nf-core\cobrameta\main.nf line 44:

    --maxk ${maxk} \
           ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --maxk "${maxk}" \

In .\modules\nf-core\cobrameta\main.nf line 45:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\cobrameta\main.nf line 46:

    --output ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}" \

In .\modules\nf-core\cobrameta\main.nf line 47:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

In .\modules\nf-core\cobrameta\main.nf line 49:

gzip ${prefix}/*.fasta
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip "${prefix}"/*.fasta

In .\modules\nf-core\cobrameta\main.nf line 50:

cat ${prefix}/*fasta.gz > ${prefix}/COBRA_all_assemblies.fasta.gz
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
cat "${prefix}"/*fasta.gz > "${prefix}"/COBRA_all_assemblies.fasta.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cobs\classicconstruct\main.nf:

In .\modules\nf-core\cobs\classicconstruct\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cobs\classicconstruct\main.nf line 28:

    --memory $task_memory_in_bytes \
             ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --memory "$task_memory_in_bytes" \

In .\modules\nf-core\cobs\classicconstruct\main.nf line 29:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\cobs\classicconstruct\main.nf line 30:

    $input \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" \

In .\modules\nf-core\cobs\classicconstruct\main.nf line 31:

    ${prefix}.index.cobs_classic
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".index.cobs_classic

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cobs\compactconstruct\main.nf:

In .\modules\nf-core\cobs\compactconstruct\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cobs\compactconstruct\main.nf line 28:

    --memory $task_memory_in_bytes \
             ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --memory "$task_memory_in_bytes" \

In .\modules\nf-core\cobs\compactconstruct\main.nf line 29:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\cobs\compactconstruct\main.nf line 30:

    $input \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" \

In .\modules\nf-core\cobs\compactconstruct\main.nf line 31:

    ${prefix}.index.cobs_compact
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".index.cobs_compact

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\concoct\concoct\main.nf:

In .\modules\nf-core\concoct\concoct\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\concoct\concoct\main.nf line 32:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\concoct\concoct\main.nf line 33:

    --coverage_file ${coverage_file} \
                    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --coverage_file "${coverage_file}" \

In .\modules\nf-core\concoct\concoct\main.nf line 34:

    --composition_file ${fasta} \
                       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --composition_file "${fasta}" \

In .\modules\nf-core\concoct\concoct\main.nf line 35:

    -b ${prefix}
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\concoct\concoctcoveragetable\main.nf:

In .\modules\nf-core\concoct\concoctcoveragetable\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\concoct\concoctcoveragetable\main.nf line 27:

    $bed \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bed" \

In .\modules\nf-core\concoct\concoctcoveragetable\main.nf line 28:

    $bamfiles \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bamfiles" \

In .\modules\nf-core\concoct\concoctcoveragetable\main.nf line 29:

    > ${prefix}.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\concoct\cutupfasta\main.nf:

In .\modules\nf-core\concoct\cutupfasta\main.nf line 30:

    $fasta \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" \

In .\modules\nf-core\concoct\cutupfasta\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\concoct\cutupfasta\main.nf line 32:

    $bedfile \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bedfile" \

In .\modules\nf-core\concoct\cutupfasta\main.nf line 33:

    > ${prefix}.fasta
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".fasta

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\concoct\extractfastabins\main.nf:

In .\modules\nf-core\concoct\extractfastabins\main.nf line 24:

mkdir ${prefix}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mkdir "${prefix}"

In .\modules\nf-core\concoct\extractfastabins\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\concoct\extractfastabins\main.nf line 28:

    $original_fasta \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$original_fasta" \

In .\modules\nf-core\concoct\extractfastabins\main.nf line 29:

    $csv \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$csv" \

In .\modules\nf-core\concoct\extractfastabins\main.nf line 30:

    --output_path ${prefix}
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output_path "${prefix}"

In .\modules\nf-core\concoct\extractfastabins\main.nf line 33:

for i in ${prefix}/*.fa; do
^-^ SC2034 (warning): i appears unused. Verify use (or export if used externally).
         ^-------^ SC2231 (info): Quote expansions in this for loop glob to prevent wordsplitting, e.g. "$dir"/*.txt .

In .\modules\nf-core\concoct\extractfastabins\main.nf line 34:

    mv \${i} \${i/\///${prefix}_}
         ^-- SC1083 (warning): This { is literal. Check expression (missing ;/\n?) or quote it.
           ^-- SC1083 (warning): This } is literal. Check expression (missing ;/\n?) or quote it.
               ^-- SC1083 (warning): This { is literal. Check expression (missing ;/\n?) or quote it.
                  ^-- SC1001 (info): This \/ will be a regular '/' in this context.
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                ^-- SC1083 (warning): This } is literal. Check expression (missing ;/\n?) or quote it.

Did you mean: 
    mv \${i} \${i/\///"${prefix}"_}

In .\modules\nf-core\concoct\extractfastabins\main.nf line 35:

    gzip \${i/\///${prefix}_}
           ^-- SC1083 (warning): This { is literal. Check expression (missing ;/\n?) or quote it.
              ^-- SC1001 (info): This \/ will be a regular '/' in this context.
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                            ^-- SC1083 (warning): This } is literal. Check expression (missing ;/\n?) or quote it.

Did you mean: 
    gzip \${i/\///"${prefix}"_}

For more information:
  https://www.shellcheck.net/wiki/SC1083 -- This { is literal. Check expressi...
  https://www.shellcheck.net/wiki/SC2034 -- i appears unused. Verify use (or ...
  https://www.shellcheck.net/wiki/SC1001 -- This \/ will be a regular '/' in ...

ShellCheck results for .\modules\nf-core\concoct\mergecutupclustering\main.nf:

In .\modules\nf-core\concoct\mergecutupclustering\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\concoct\mergecutupclustering\main.nf line 27:

    $clustering_csv \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$clustering_csv" \

In .\modules\nf-core\concoct\mergecutupclustering\main.nf line 28:

    > ${prefix}.csv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".csv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\conifer\main.nf:

In .\modules\nf-core\conifer\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\conifer\main.nf line 27:

    --input $kraken_result \
            ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$kraken_result" \

In .\modules\nf-core\conifer\main.nf line 28:

    --db $kraken_taxon_db > ${prefix}.score
         ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --db "$kraken_taxon_db" > "${prefix}".score

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\controlfreec\assesssignificance\main.nf:

In .\modules\nf-core\controlfreec\assesssignificance\main.nf line 25:

cat \$(which assess_significance.R) | R --slave --args ${cnvs} ${ratio}
      ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
      ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\controlfreec\freec\main.nf:

In .\modules\nf-core\controlfreec\freec\main.nf line 97:

echo "[general]" >> config.txt
^----------------------------^ SC2129 (style): Consider using { cmd1; cmd2; } >> file instead of individual redirects.

In .\modules\nf-core\controlfreec\freec\main.nf line 98:

echo ${bedgraphoutput} >> config.txt
     ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${bedgraphoutput}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 99:

echo ${breakpointthreshold} >> config.txt
     ^--------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${breakpointthreshold}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 100:

echo ${breakpointtype} >> config.txt
     ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${breakpointtype}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 101:

echo ${chr_files} >> config.txt
     ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${chr_files}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 102:

echo ${chr_length} >> config.txt
     ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${chr_length}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 103:

echo ${coefficientofvariation} >> config.txt
     ^-----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${coefficientofvariation}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 104:

echo ${contamination} >> config.txt
     ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${contamination}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 105:

echo ${contaminationadjustment} >> config.txt
     ^------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${contaminationadjustment}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 106:

echo ${degree} >> config.txt
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${degree}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 107:

echo ${forcegccontentnormalization} >> config.txt
     ^----------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${forcegccontentnormalization}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 108:

echo ${gccontentprofile} >> config.txt
     ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${gccontentprofile}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 109:

echo ${mappability} >> config.txt
     ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${mappability}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 110:

echo ${intercept} >> config.txt
     ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${intercept}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 111:

echo ${mincnalength} >> config.txt
     ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${mincnalength}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 112:

echo ${minmappabilityperwindow} >> config.txt
     ^------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${minmappabilityperwindow}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 113:

echo ${minexpectedgc} >> config.txt
     ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${minexpectedgc}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 114:

echo ${maxexpectedgc} >> config.txt
     ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${maxexpectedgc}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 115:

echo ${minimalsubclonepresence} >> config.txt
     ^------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${minimalsubclonepresence}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 117:

echo ${noisydata} >> config.txt
     ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${noisydata}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 118:

echo ${output} >> config.txt
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${output}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 119:

echo ${ploidy} >> config.txt
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${ploidy}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 120:

echo ${printNA} >> config.txt
     ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${printNA}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 121:

echo ${readcountthreshold} >> config.txt
     ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${readcountthreshold}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 122:

echo ${sex} >> config.txt
     ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${sex}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 123:

echo ${step} >> config.txt
     ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${step}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 124:

echo ${telocentromeric} >> config.txt
     ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${telocentromeric}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 125:

echo ${uniquematch} >> config.txt
     ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${uniquematch}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 126:

echo ${window} >> config.txt
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${window}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 129:

echo ${matefile_normal} >> config.txt
     ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${matefile_normal}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 130:

echo ${matecopynumberfile_normal} >> config.txt
     ^--------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${matecopynumberfile_normal}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 131:

echo ${minipileup_normal} >> config.txt
     ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${minipileup_normal}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 132:

echo ${inputformat_normal} >> config.txt
     ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${inputformat_normal}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 133:

echo ${mateorientation_normal} >> config.txt
     ^-----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${mateorientation_normal}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 136:

echo ${matefile_tumor} >> config.txt
     ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${matefile_tumor}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 137:

echo ${matecopynumberfile_tumor} >> config.txt
     ^-------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${matecopynumberfile_tumor}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 138:

echo ${minipileup_tumor} >> config.txt
     ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${minipileup_tumor}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 139:

echo ${inputformat_tumor} >> config.txt
     ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${inputformat_tumor}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 140:

echo ${mateorientation_tumor} >> config.txt
     ^----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${mateorientation_tumor}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 143:

echo ${makepileup} >> config.txt
     ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${makepileup}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 144:

echo ${fastafile} >> config.txt
     ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${fastafile}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 145:

echo ${minimalcoverageperposition} >> config.txt
     ^---------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${minimalcoverageperposition}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 146:

echo ${minimalqualityperposition} >> config.txt
     ^--------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${minimalqualityperposition}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 147:

echo ${shiftinquality} >> config.txt
     ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${shiftinquality}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 148:

echo ${snpfile} >> config.txt
     ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${snpfile}" >> config.txt

In .\modules\nf-core\controlfreec\freec\main.nf line 151:

echo ${target_bed} >> config.txt
     ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "${target_bed}" >> config.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2129 -- Consider using { cmd1; cmd2; } >>...

ShellCheck results for .\modules\nf-core\controlfreec\freec2bed\main.nf:

In .\modules\nf-core\controlfreec\freec2bed\main.nf line 25:

freec2bed.pl -f ${ratio} ${args} > ${prefix}.bed
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                         ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
freec2bed.pl -f "${ratio}" "${args}" > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\controlfreec\freec2circos\main.nf:

In .\modules\nf-core\controlfreec\freec2circos\main.nf line 25:

freec2circos.pl -f ${ratio} ${args} > ${prefix}.circos.txt
                   ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                            ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
freec2circos.pl -f "${ratio}" "${args}" > "${prefix}".circos.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\controlfreec\makegraph\main.nf:

In .\modules\nf-core\controlfreec\makegraph\main.nf line 29:

cat \$(which makeGraph.R) | R --slave --args ${ploidy} ${args} ${ratio} ${baf}
      ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
      ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\controlfreec\makegraph2\main.nf:

In .\modules\nf-core\controlfreec\makegraph2\main.nf line 29:

cat \$(which makeGraph2.0.R) | R --slave --args ${args} ${ratio} ${baf}
      ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
      ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\cooler\balance\main.nf:

In .\modules\nf-core\cooler\balance\main.nf line 27:

ln -s ${cool} ${prefix}.${extension}
      ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
ln -s "${cool}" "${prefix}"."${extension}"

In .\modules\nf-core\cooler\balance\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cooler\balance\main.nf line 31:

    -p ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${task.cpus}" \

In .\modules\nf-core\cooler\balance\main.nf line 32:

    ${prefix}.${extension}${suffix}
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"."${extension}""${suffix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cooler\cload\main.nf:

In .\modules\nf-core\cooler\cload\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cooler\cload\main.nf line 29:

    $nproc \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$nproc" \

In .\modules\nf-core\cooler\cload\main.nf line 30:

    ${chromsizes}:${cool_bin} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                  ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${chromsizes}":"${cool_bin}" \

In .\modules\nf-core\cooler\cload\main.nf line 31:

    $pairs \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$pairs" \

In .\modules\nf-core\cooler\cload\main.nf line 32:

    ${prefix}.cool
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".cool

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cooler\digest\main.nf:

In .\modules\nf-core\cooler\digest\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cooler\digest\main.nf line 28:

    $chromsizes \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$chromsizes" \

In .\modules\nf-core\cooler\digest\main.nf line 29:

    $fasta \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" \

In .\modules\nf-core\cooler\digest\main.nf line 30:

    $enzyme
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$enzyme"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cooler\dump\main.nf:

In .\modules\nf-core\cooler\dump\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cooler\dump\main.nf line 27:

    -o ${prefix}.bedpe \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".bedpe \

In .\modules\nf-core\cooler\dump\main.nf line 28:

    $cool$suffix
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
         ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$cool""$suffix"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cooler\makebins\main.nf:

In .\modules\nf-core\cooler\makebins\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cooler\makebins\main.nf line 26:

    ${chromsizes} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${chromsizes}" \

In .\modules\nf-core\cooler\makebins\main.nf line 27:

    ${cool_bin} > ${prefix}.bed
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${cool_bin}" > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cooler\merge\main.nf:

In .\modules\nf-core\cooler\merge\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cooler\merge\main.nf line 26:

    ${prefix}.cool \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".cool \

In .\modules\nf-core\cooler\merge\main.nf line 27:

    ${cool}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${cool}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cooler\zoomify\main.nf:

In .\modules\nf-core\cooler\zoomify\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cooler\zoomify\main.nf line 26:

    -n $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -n "$task".cpus \

In .\modules\nf-core\cooler\zoomify\main.nf line 27:

    -o ${prefix}.mcool \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".mcool \

In .\modules\nf-core\cooler\zoomify\main.nf line 28:

    $cool
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$cool"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\coptr\estimate\main.nf:

In .\modules\nf-core\coptr\estimate\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\coptr\extract\main.nf:

In .\modules\nf-core\coptr\extract\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\coptr\index\main.nf:

In .\modules\nf-core\coptr\index\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\coptr\index\main.nf line 29:

    --bt2-threads $task.cpus \
                  ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bt2-threads "$task".cpus \

In .\modules\nf-core\coptr\index\main.nf line 31:

    bowtie2/${prefix}
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    bowtie2/"${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\coptr\map\main.nf:

In .\modules\nf-core\coptr\map\main.nf line 31:

INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\.rev.1.bt2\$//"`
      ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
INDEX=$(find -L ./ -name "*.rev.1.bt2" | sed "s/\.rev.1.bt2\$//")

In .\modules\nf-core\coptr\map\main.nf line 32:

[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\.rev.1.bt2l\$//"`
      ^-----^ SC2157 (error): Argument to -z is always false due to literal strings.
                    ^---^ SC2034 (warning): INDEX appears unused. Verify use (or export if used externally).
                          ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
[ -z "\$INDEX" ] && INDEX=$(find -L ./ -name "*.rev.1.bt2l" | sed "s/\.rev.1.bt2l\$//")

In .\modules\nf-core\coptr\map\main.nf line 33:

[ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
      ^-----^ SC2157 (error): Argument to -z is always false due to literal strings.

In .\modules\nf-core\coptr\map\main.nf line 37:

    $args $paired_end \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
          ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" "$paired_end" \

In .\modules\nf-core\coptr\map\main.nf line 38:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\coptr\map\main.nf line 43:

mv ${prefix}.bam ${prefix}_${prefix2}.bam
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                           ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${prefix}".bam "${prefix}"_"${prefix2}".bam

For more information:
  https://www.shellcheck.net/wiki/SC2157 -- Argument to -z is always false du...
  https://www.shellcheck.net/wiki/SC2034 -- INDEX appears unused. Verify use ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\coptr\merge\main.nf:

In .\modules\nf-core\coptr\merge\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\coptr\merge\main.nf line 28:

    ${input_bams} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_bams}" \

In .\modules\nf-core\coptr\merge\main.nf line 29:

    ${prefix}.bam
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".bam

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\coreograph\main.nf:

In .\modules\nf-core\coreograph\main.nf line 29:

    --imagePath ${image} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --imagePath "${image}" \

In .\modules\nf-core\coreograph\main.nf line 31:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\coverm\contig\main.nf:

In .\modules\nf-core\coverm\contig\main.nf line 33:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\coverm\contig\main.nf line 34:

    ${input_type} ${input} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                  ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_type}" "${input}" \

In .\modules\nf-core\coverm\contig\main.nf line 35:

    ${reference_str} \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reference_str}" \

In .\modules\nf-core\coverm\contig\main.nf line 36:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\coverm\contig\main.nf line 37:

    --output-file ${prefix}.depth.txt
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-file "${prefix}".depth.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\crabz\compress\main.nf:

In .\modules\nf-core\crabz\compress\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\crabz\compress\main.nf line 26:

    -p $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "$task".cpus \

In .\modules\nf-core\crabz\compress\main.nf line 27:

    -o ${prefix}.gz \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".gz \

In .\modules\nf-core\crabz\compress\main.nf line 28:

    $file
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$file"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\crabz\decompress\main.nf:

In .\modules\nf-core\crabz\decompress\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\crabz\decompress\main.nf line 26:

    -p $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "$task".cpus \

In .\modules\nf-core\crabz\decompress\main.nf line 27:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\crabz\decompress\main.nf line 28:

    $archive
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$archive"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\crisprcleanr\normalize\main.nf:

In .\modules\nf-core\crisprcleanr\normalize\main.nf line 27:

#!/usr/bin/env Rscript
^-- SC1128 (error): The shebang must be on the first line. Delete blanks and move comments.

In .\modules\nf-core\crisprcleanr\normalize\main.nf line 28:

library(CRISPRcleanR)
^-- SC1073 (error): Couldn't parse this function. Fix to allow more checks.
        ^-- SC1065 (error): Trying to declare parameters? Don't. Use () and refer to params as $1, $2..

In .\modules\nf-core\crisprcleanr\normalize\main.nf line 29:

library <- read.delim('${library_file}', header=T,sep="\t")
^-- SC1064 (error): Expected a { to open the function definition.
^-- SC1072 (error):  Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1064 -- Expected a { to open the function...
  https://www.shellcheck.net/wiki/SC1065 -- Trying to declare parameters? Don...
  https://www.shellcheck.net/wiki/SC1128 -- The shebang must be on the first ...

ShellCheck results for .\modules\nf-core\crumble\main.nf:

In .\modules\nf-core\crumble\main.nf line 39:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\crumble\main.nf line 40:

    $bedin \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bedin" \

In .\modules\nf-core\crumble\main.nf line 41:

    $bedout \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bedout" \

In .\modules\nf-core\crumble\main.nf line 42:

    $input \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" \

In .\modules\nf-core\crumble\main.nf line 43:

    ${prefix}.${extension}
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"."${extension}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\csvtk\concat\main.nf:

In .\modules\nf-core\csvtk\concat\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\csvtk\concat\main.nf line 32:

    --num-cpus $task.cpus \
               ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --num-cpus "$task".cpus \

In .\modules\nf-core\csvtk\concat\main.nf line 35:

    --out-file ${prefix}.${out_extension} \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                         ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --out-file "${prefix}"."${out_extension}" \

In .\modules\nf-core\csvtk\concat\main.nf line 36:

    $csv
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$csv"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\csvtk\join\main.nf:

In .\modules\nf-core\csvtk\join\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\csvtk\join\main.nf line 28:

    --num-cpus $task.cpus \
               ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --num-cpus "$task".cpus \

In .\modules\nf-core\csvtk\join\main.nf line 29:

    --out-file ${prefix}.${out_extension} \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                         ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --out-file "${prefix}"."${out_extension}" \

In .\modules\nf-core\csvtk\join\main.nf line 30:

    $csv
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$csv"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\csvtk\split\main.nf:

In .\modules\nf-core\csvtk\split\main.nf line 29:

sed -i.bak '/^##/d' $csv
                    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
sed -i.bak '/^##/d' "$csv"

In .\modules\nf-core\csvtk\split\main.nf line 32:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\csvtk\split\main.nf line 33:

    --num-cpus $task.cpus \
               ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --num-cpus "$task".cpus \

In .\modules\nf-core\csvtk\split\main.nf line 34:

    $delimiter \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$delimiter" \

In .\modules\nf-core\csvtk\split\main.nf line 35:

    $out_delimiter \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$out_delimiter" \

In .\modules\nf-core\csvtk\split\main.nf line 36:

    $csv
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$csv"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\custom\addmostsevereconsequence\main.nf:

In .\modules\nf-core\custom\addmostsevereconsequence\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\custom\addmostsevereconsequence\main.nf line 31:

    --file_in $vcf \
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --file_in "$vcf" \

In .\modules\nf-core\custom\addmostsevereconsequence\main.nf line 32:

    --file_out ${prefix}.vcf \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --file_out "${prefix}".vcf \

In .\modules\nf-core\custom\addmostsevereconsequence\main.nf line 33:

    --variant_csq $variant_consequences
                  ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant_csq "$variant_consequences"

In .\modules\nf-core\custom\addmostsevereconsequence\main.nf line 36:

    $args2 \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2" \

In .\modules\nf-core\custom\addmostsevereconsequence\main.nf line 37:

    --threads ${task.cpus-1} \
              ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus-1}" \

In .\modules\nf-core\custom\addmostsevereconsequence\main.nf line 38:

    ${prefix}.vcf
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".vcf

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\custom\addmostseverepli\main.nf:

In .\modules\nf-core\custom\addmostseverepli\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\custom\addmostseverepli\main.nf line 29:

    --file_in $vcf \
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --file_in "$vcf" \

In .\modules\nf-core\custom\addmostseverepli\main.nf line 30:

    --file_out ${prefix}.vcf
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --file_out "${prefix}".vcf

In .\modules\nf-core\custom\addmostseverepli\main.nf line 33:

    $args2 \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2" \

In .\modules\nf-core\custom\addmostseverepli\main.nf line 34:

    --threads ${task.cpus-1} \
              ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus-1}" \

In .\modules\nf-core\custom\addmostseverepli\main.nf line 35:

    ${prefix}.vcf
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".vcf

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\custom\filterdifferentialtable\main.nf:

In .\modules\nf-core\custom\filterdifferentialtable\main.nf line 26:

#!/usr/bin/env python
^-- SC1128 (error): The shebang must be on the first line. Delete blanks and move comments.

In .\modules\nf-core\custom\filterdifferentialtable\main.nf line 32:

if not "${input_file}".lower().endswith(('.csv', '.tsv', '.txt')):
^-- SC1073 (error): Couldn't parse this if expression. Fix to allow more checks.
                            ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
                            ^-- SC1050 (error): Expected 'then'.
                            ^-- SC1072 (error): Expected 'then'. Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1050 -- Expected 'then'.
  https://www.shellcheck.net/wiki/SC1128 -- The shebang must be on the first ...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...

ShellCheck results for .\modules\nf-core\custom\getchromsizes\main.nf:

In .\modules\nf-core\custom\getchromsizes\main.nf line 25:

samtools faidx $fasta
               ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
samtools faidx "$fasta"

In .\modules\nf-core\custom\getchromsizes\main.nf line 26:

cut -f 1,2 ${fasta}.fai > ${fasta}.sizes
           ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
cut -f 1,2 "${fasta}".fai > "${fasta}".sizes

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\custom\gtffilter\main.nf:

In .\modules\nf-core\custom\gtffilter\main.nf line 30:

touch ${prefix}.${suffix}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}"."${suffix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\custom\matrixfilter\main.nf:

In .\modules\nf-core\custom\matrixfilter\main.nf line 34:

touch ${prefix}.filtered.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".filtered.tsv

In .\modules\nf-core\custom\matrixfilter\main.nf line 35:

touch ${prefix}.tests.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".tests.tsv

In .\modules\nf-core\custom\matrixfilter\main.nf line 36:

touch ${prefix}.R_sessionInfo.log
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".R_sessionInfo.log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\custom\tabulartogseachip\main.nf:

In .\modules\nf-core\custom\tabulartogseachip\main.nf line 25:

    file=\$1
    ^--^ SC2034 (warning): file appears unused. Verify use (or export if used externally).

In .\modules\nf-core\custom\tabulartogseachip\main.nf line 26:

    column=\$2
    ^----^ SC2034 (warning): column appears unused. Verify use (or export if used externally).

In .\modules\nf-core\custom\tabulartogseachip\main.nf line 31:

id_col=\$(find_column_number $tabular $id)
^----^ SC2034 (warning): id_col appears unused. Verify use (or export if used externally).
         ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
         ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- column appears unused. Verify use...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\custom\tabulartogseacls\main.nf:

In .\modules\nf-core\custom\tabulartogseacls\main.nf line 30:

cls_file=${prefix}.cls
^------^ SC2034 (warning): cls_file appears unused. Verify use (or export if used externally).

In .\modules\nf-core\custom\tabulartogseacls\main.nf line 32:

column_number=\$(cat ${samples} | head -n 1 | tr '${separator}' "\n" | grep -En "^${variable}\$" | awk -F':' '{print \$1}')
^-----------^ SC2034 (warning): column_number appears unused. Verify use (or export if used externally).
                ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
                ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- cls_file appears unused. Verify u...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\custom\tabulartogseagct\main.nf:

In .\modules\nf-core\custom\tabulartogseagct\main.nf line 27:

n_columns=\$(head -n 1 ${tabular} | tr "${separator}" "\n" | wc -l)
^-------^ SC2034 (warning): n_columns appears unused. Verify use (or export if used externally).
            ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
            ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- n_columns appears unused. Verify ...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\custom\tx2gene\main.nf:

In .\modules\nf-core\custom\tx2gene\main.nf line 29:

touch ${meta.id}.tx2gene.tsv
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}".tx2gene.tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cutadapt\main.nf:

In .\modules\nf-core\cutadapt\main.nf line 28:

    --cores $task.cpus \
            ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cores "$task".cpus \

In .\modules\nf-core\cutadapt\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\cutadapt\main.nf line 30:

    $trimmed \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$trimmed" \

In .\modules\nf-core\cutadapt\main.nf line 31:

    $reads \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads" \

In .\modules\nf-core\cutadapt\main.nf line 32:

    > ${prefix}.cutadapt.log
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".cutadapt.log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\cutesv\main.nf:

In .\modules\nf-core\cutesv\main.nf line 26:

    ${bam} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bam}" \

In .\modules\nf-core\cutesv\main.nf line 27:

    ${fasta} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fasta}" \

In .\modules\nf-core\cutesv\main.nf line 28:

    ${prefix}.vcf \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".vcf \

In .\modules\nf-core\cutesv\main.nf line 30:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\cutesv\main.nf line 31:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\damageprofiler\main.nf:

In .\modules\nf-core\damageprofiler\main.nf line 30:

    -i $bam \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bam" \

In .\modules\nf-core\damageprofiler\main.nf line 31:

    -o $prefix/ \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "$prefix"/ \

In .\modules\nf-core\damageprofiler\main.nf line 32:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\damageprofiler\main.nf line 33:

    $reference \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference" \

In .\modules\nf-core\damageprofiler\main.nf line 34:

    $species_list
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$species_list"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dastool\dastool\main.nf:

In .\modules\nf-core\dastool\dastool\main.nf line 47:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\dastool\dastool\main.nf line 48:

    $proteins_pred \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$proteins_pred" \

In .\modules\nf-core\dastool\dastool\main.nf line 49:

    $db_dir \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$db_dir" \

In .\modules\nf-core\dastool\dastool\main.nf line 50:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\dastool\dastool\main.nf line 51:

    -i $bin_list \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bin_list" \

In .\modules\nf-core\dastool\dastool\main.nf line 52:

    -c $clean_contigs \
       ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -c "$clean_contigs" \

In .\modules\nf-core\dastool\dastool\main.nf line 53:

    -o $prefix
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "$prefix"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dastool\fastatocontig2bin\main.nf:

In .\modules\nf-core\dastool\fastatocontig2bin\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\dastool\fastatocontig2bin\main.nf line 33:

    -e $file_extension \
       ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -e "$file_extension" \

In .\modules\nf-core\dastool\fastatocontig2bin\main.nf line 34:

    > ${prefix}.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\datavzrd\main.nf:

In .\modules\nf-core\datavzrd\main.nf line 24:

mkdir ${prefix}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mkdir "${prefix}"

In .\modules\nf-core\datavzrd\main.nf line 26:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\datavzrd\main.nf line 27:

    ${config_file} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${config_file}" \

In .\modules\nf-core\datavzrd\main.nf line 28:

    --output ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dedup\main.nf:

In .\modules\nf-core\dedup\main.nf line 29:

    -Xmx${task.memory.toGiga()}g  \
        ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${task.memory.toGiga()}"g  \

In .\modules\nf-core\dedup\main.nf line 30:

    -i $bam \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bam" \

In .\modules\nf-core\dedup\main.nf line 32:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeparg\downloaddata\main.nf:

In .\modules\nf-core\deeparg\downloaddata\main.nf line 42:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeparg\predict\main.nf:

In .\modules\nf-core\deeparg\predict\main.nf line 42:

DATABASE=`find -L ${db} -type d -name "database" | sed 's/database//'`
^------^ SC2034 (warning): DATABASE appears unused. Verify use (or export if used externally).
         ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.
                  ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
DATABASE=$(find -L "${db}" -type d -name "database" | sed 's/database//')

In .\modules\nf-core\deeparg\predict\main.nf line 52:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\deeparg\predict\main.nf line 53:

    -i ${fasta} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${fasta}" \

In .\modules\nf-core\deeparg\predict\main.nf line 54:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\deeparg\predict\main.nf line 56:

    --model ${model}
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --model "${model}"

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- DATABASE appears unused. Verify u...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\deepbgc\pipeline\main.nf:

In .\modules\nf-core\deepbgc\pipeline\main.nf line 46:

for i in \$(find -name '${genome.baseName}*' -type f); do
^-- SC1073 (error): Couldn't parse this for loop. Fix to allow more checks.
           ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
           ^-- SC1058 (error): Expected 'do'.
           ^-- SC1072 (error): Expected 'do'. Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1058 -- Expected 'do'.
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1072 -- Expected 'do'. Fix any mentioned ...

ShellCheck results for .\modules\nf-core\deepcell\mesmer\main.nf:

In .\modules\nf-core\deepcell\mesmer\main.nf line 28:

    --nuclear-image $img \
                    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nuclear-image "$img" \

In .\modules\nf-core\deepcell\mesmer\main.nf line 30:

    --output-name ${prefix}.tif \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-name "${prefix}".tif \

In .\modules\nf-core\deepcell\mesmer\main.nf line 31:

    $membrane_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$membrane_command" \

In .\modules\nf-core\deepcell\mesmer\main.nf line 32:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deepsomatic\main.nf:

In .\modules\nf-core\deepsomatic\main.nf line 35:

    --ref=${fasta} \
          ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ref="${fasta}" \

In .\modules\nf-core\deepsomatic\main.nf line 36:

    --reads_normal=${input_normal} \
                   ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reads_normal="${input_normal}" \

In .\modules\nf-core\deepsomatic\main.nf line 37:

    --reads_tumor=${input_tumor} \
                  ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reads_tumor="${input_tumor}" \

In .\modules\nf-core\deepsomatic\main.nf line 38:

    --output_vcf=${prefix}.vcf.gz \
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output_vcf="${prefix}".vcf.gz \

In .\modules\nf-core\deepsomatic\main.nf line 39:

    --output_gvcf=${prefix}.g.vcf.gz \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output_gvcf="${prefix}".g.vcf.gz \

In .\modules\nf-core\deepsomatic\main.nf line 42:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\deepsomatic\main.nf line 43:

    ${regions} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions}" \

In .\modules\nf-core\deepsomatic\main.nf line 45:

    --num_shards=${task.cpus}
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --num_shards="${task.cpus}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeptmhmm\main.nf:

In .\modules\nf-core\deeptmhmm\main.nf line 32:

    gzip -c -d $fasta > $fasta_name
               ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "$fasta" > "$fasta_name"

In .\modules\nf-core\deeptmhmm\main.nf line 38:

    --fasta ${fasta_name} \
            ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fasta "${fasta_name}" \

In .\modules\nf-core\deeptmhmm\main.nf line 39:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeptools\alignmentsieve\main.nf:

In .\modules\nf-core\deeptools\alignmentsieve\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\deeptools\alignmentsieve\main.nf line 27:

    -b $input \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "$input" \

In .\modules\nf-core\deeptools\alignmentsieve\main.nf line 28:

    -o ${prefix}_as.bam \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}"_as.bam \

In .\modules\nf-core\deeptools\alignmentsieve\main.nf line 29:

    --filterMetrics ${prefix}_log.txt \
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --filterMetrics "${prefix}"_log.txt \

In .\modules\nf-core\deeptools\alignmentsieve\main.nf line 30:

    --numberOfProcessors $task.cpus
                         ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --numberOfProcessors "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeptools\bamcoverage\main.nf:

In .\modules\nf-core\deeptools\bamcoverage\main.nf line 36:

samtools view -T $fasta $input $fai_reference -@ $task.cpus -o $input_out
                 ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                               ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                               ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
samtools view -T "$fasta" "$input" "$fai_reference" -@ "$task".cpus -o "$input_out"

In .\modules\nf-core\deeptools\bamcoverage\main.nf line 37:

samtools index -b $input_out -@ $task.cpus
                  ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
samtools index -b "$input_out" -@ "$task".cpus

In .\modules\nf-core\deeptools\bamcoverage\main.nf line 40:

    --bam $input_out \
          ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bam "$input_out" \

In .\modules\nf-core\deeptools\bamcoverage\main.nf line 41:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\deeptools\bamcoverage\main.nf line 42:

    --numberOfProcessors ${task.cpus} \
                         ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --numberOfProcessors "${task.cpus}" \

In .\modules\nf-core\deeptools\bamcoverage\main.nf line 43:

    --outFileName ${prefix}.${extension}
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outFileName "${prefix}"."${extension}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeptools\computematrix\main.nf:

In .\modules\nf-core\deeptools\computematrix\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\deeptools\computematrix\main.nf line 28:

    --regionsFileName $bed \
                      ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --regionsFileName "$bed" \

In .\modules\nf-core\deeptools\computematrix\main.nf line 29:

    --scoreFileName $bigwig \
                    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --scoreFileName "$bigwig" \

In .\modules\nf-core\deeptools\computematrix\main.nf line 30:

    --outFileName ${prefix}.computeMatrix.mat.gz \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outFileName "${prefix}".computeMatrix.mat.gz \

In .\modules\nf-core\deeptools\computematrix\main.nf line 31:

    --outFileNameMatrix ${prefix}.computeMatrix.vals.mat.tab \
                        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outFileNameMatrix "${prefix}".computeMatrix.vals.mat.tab \

In .\modules\nf-core\deeptools\computematrix\main.nf line 32:

    --numberOfProcessors $task.cpus
                         ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --numberOfProcessors "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeptools\multibamsummary\main.nf:

In .\modules\nf-core\deeptools\multibamsummary\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\deeptools\multibamsummary\main.nf line 27:

    $label \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$label" \

In .\modules\nf-core\deeptools\multibamsummary\main.nf line 28:

    --bamfiles ${bams.join(' ')} \
               ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bamfiles "${bams.join(' ')}" \

In .\modules\nf-core\deeptools\multibamsummary\main.nf line 29:

    --numberOfProcessors $task.cpus \
                         ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --numberOfProcessors "$task".cpus \

In .\modules\nf-core\deeptools\multibamsummary\main.nf line 30:

    --outFileName ${prefix}.bamSummary.npz
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outFileName "${prefix}".bamSummary.npz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeptools\plotcorrelation\main.nf:

In .\modules\nf-core\deeptools\plotcorrelation\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\deeptools\plotcorrelation\main.nf line 31:

    --corData $matrix \
              ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --corData "$matrix" \

In .\modules\nf-core\deeptools\plotcorrelation\main.nf line 32:

    --corMethod $resolved_method \
                ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --corMethod "$resolved_method" \

In .\modules\nf-core\deeptools\plotcorrelation\main.nf line 33:

    --whatToPlot $resolved_plot_type \
                 ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --whatToPlot "$resolved_plot_type" \

In .\modules\nf-core\deeptools\plotcorrelation\main.nf line 34:

    --plotFile ${prefix}.plotCorrelation.pdf \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --plotFile "${prefix}".plotCorrelation.pdf \

In .\modules\nf-core\deeptools\plotcorrelation\main.nf line 35:

    --outFileCorMatrix ${prefix}.plotCorrelation.mat.tab
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outFileCorMatrix "${prefix}".plotCorrelation.mat.tab

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeptools\plotfingerprint\main.nf:

In .\modules\nf-core\deeptools\plotfingerprint\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\deeptools\plotfingerprint\main.nf line 29:

    $extend \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$extend" \

In .\modules\nf-core\deeptools\plotfingerprint\main.nf line 30:

    --bamfiles ${bams.join(' ')} \
               ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bamfiles "${bams.join(' ')}" \

In .\modules\nf-core\deeptools\plotfingerprint\main.nf line 31:

    --plotFile ${prefix}.plotFingerprint.pdf \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --plotFile "${prefix}".plotFingerprint.pdf \

In .\modules\nf-core\deeptools\plotfingerprint\main.nf line 32:

    --outRawCounts ${prefix}.plotFingerprint.raw.txt \
                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outRawCounts "${prefix}".plotFingerprint.raw.txt \

In .\modules\nf-core\deeptools\plotfingerprint\main.nf line 33:

    --outQualityMetrics ${prefix}.plotFingerprint.qcmetrics.txt \
                        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outQualityMetrics "${prefix}".plotFingerprint.qcmetrics.txt \

In .\modules\nf-core\deeptools\plotfingerprint\main.nf line 34:

    --numberOfProcessors $task.cpus
                         ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --numberOfProcessors "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeptools\plotheatmap\main.nf:

In .\modules\nf-core\deeptools\plotheatmap\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\deeptools\plotheatmap\main.nf line 27:

    --matrixFile $matrix \
                 ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --matrixFile "$matrix" \

In .\modules\nf-core\deeptools\plotheatmap\main.nf line 28:

    --outFileName ${prefix}.plotHeatmap.pdf \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outFileName "${prefix}".plotHeatmap.pdf \

In .\modules\nf-core\deeptools\plotheatmap\main.nf line 29:

    --outFileNameMatrix ${prefix}.plotHeatmap.mat.tab
                        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outFileNameMatrix "${prefix}".plotHeatmap.mat.tab

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeptools\plotpca\main.nf:

In .\modules\nf-core\deeptools\plotpca\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\deeptools\plotpca\main.nf line 27:

    --corData $matrix \
              ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --corData "$matrix" \

In .\modules\nf-core\deeptools\plotpca\main.nf line 28:

    --plotFile ${prefix}.plotPCA.pdf \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --plotFile "${prefix}".plotPCA.pdf \

In .\modules\nf-core\deeptools\plotpca\main.nf line 29:

    --outFileNameData ${prefix}.plotPCA.tab
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outFileNameData "${prefix}".plotPCA.tab

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deeptools\plotprofile\main.nf:

In .\modules\nf-core\deeptools\plotprofile\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\deeptools\plotprofile\main.nf line 27:

    --matrixFile $matrix \
                 ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --matrixFile "$matrix" \

In .\modules\nf-core\deeptools\plotprofile\main.nf line 28:

    --outFileName ${prefix}.plotProfile.pdf \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outFileName "${prefix}".plotProfile.pdf \

In .\modules\nf-core\deeptools\plotprofile\main.nf line 29:

    --outFileNameData ${prefix}.plotProfile.tab
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outFileNameData "${prefix}".plotProfile.tab

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deepvariant\callvariants\main.nf:

In .\modules\nf-core\deepvariant\callvariants\main.nf line 38:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deepvariant\makeexamples\main.nf:

In .\modules\nf-core\deepvariant\makeexamples\main.nf line 35:

seq 0 ${task.cpus - 1} | parallel -q --halt 2 --line-buffer /opt/deepvariant/bin/make_examples \
      ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
seq 0 "${task.cpus - 1}" | parallel -q --halt 2 --line-buffer /opt/deepvariant/bin/make_examples \

In .\modules\nf-core\deepvariant\makeexamples\main.nf line 41:

    ${regions} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions}" \

In .\modules\nf-core\deepvariant\makeexamples\main.nf line 42:

    ${par_regions} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${par_regions}" \

In .\modules\nf-core\deepvariant\makeexamples\main.nf line 43:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deepvariant\postprocessvariants\main.nf:

In .\modules\nf-core\deepvariant\postprocessvariants\main.nf line 61:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\deepvariant\postprocessvariants\main.nf line 67:

    ${regions} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions}" \

In .\modules\nf-core\deepvariant\postprocessvariants\main.nf line 68:

    ${small_model_arg} \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${small_model_arg}" \

In .\modules\nf-core\deepvariant\postprocessvariants\main.nf line 69:

    --cpus $task.cpus
           ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpus "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deepvariant\rundeepvariant\main.nf:

In .\modules\nf-core\deepvariant\rundeepvariant\main.nf line 40:

    --ref=${fasta} \
          ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ref="${fasta}" \

In .\modules\nf-core\deepvariant\rundeepvariant\main.nf line 41:

    --reads=${input} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reads="${input}" \

In .\modules\nf-core\deepvariant\rundeepvariant\main.nf line 42:

    --output_vcf=${prefix}.vcf.gz \
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output_vcf="${prefix}".vcf.gz \

In .\modules\nf-core\deepvariant\rundeepvariant\main.nf line 43:

    --output_gvcf=${prefix}.g.vcf.gz \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output_gvcf="${prefix}".g.vcf.gz \

In .\modules\nf-core\deepvariant\rundeepvariant\main.nf line 44:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\deepvariant\rundeepvariant\main.nf line 45:

    ${regions} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions}" \

In .\modules\nf-core\deepvariant\rundeepvariant\main.nf line 46:

    ${par_regions} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${par_regions}" \

In .\modules\nf-core\deepvariant\rundeepvariant\main.nf line 48:

    --num_shards=${task.cpus}
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --num_shards="${task.cpus}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deepvariant\vcfstatsreport\main.nf:

In .\modules\nf-core\deepvariant\vcfstatsreport\main.nf line 29:

    --input_vcf=${vcf} \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input_vcf="${vcf}" \

In .\modules\nf-core\deepvariant\vcfstatsreport\main.nf line 30:

    --outfile_base ${prefix}
                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outfile_base "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\delly\call\main.nf:

In .\modules\nf-core\delly\call\main.nf line 39:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\delly\call\main.nf line 40:

    ${bcf_output} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bcf_output}" \

In .\modules\nf-core\delly\call\main.nf line 41:

    --genome ${fasta} \
             ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --genome "${fasta}" \

In .\modules\nf-core\delly\call\main.nf line 42:

    ${genotype} \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${genotype}" \

In .\modules\nf-core\delly\call\main.nf line 43:

    ${exclude} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${exclude}" \

In .\modules\nf-core\delly\call\main.nf line 44:

    ${input} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input}" \

In .\modules\nf-core\delly\call\main.nf line 45:

    ${vcf_output}
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcf_output}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\demuxem\main.nf:

In .\modules\nf-core\demuxem\main.nf line 30:

demuxEM $input_raw_gene_bc_matrices_h5 \
        ^----------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
demuxEM "$input_raw_gene_bc_matrices_h5" \

In .\modules\nf-core\demuxem\main.nf line 31:

$input_hto_csv_file $output_name \
^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
"$input_hto_csv_file" "$output_name" \

In .\modules\nf-core\demuxem\main.nf line 32:

$args \
^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
"$args" \

In .\modules\nf-core\demuxem\main.nf line 33:

$generateGenderPlot\
^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
"$generateGenderPlot"\

In .\modules\nf-core\demuxem\main.nf line 34:

$genome_file\
^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
"$genome_file"\

In .\modules\nf-core\demuxem\main.nf line 35:

$diagnostic_plots
^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
"$diagnostic_plots"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\deseq2\differential\main.nf:

In .\modules\nf-core\deseq2\differential\main.nf line 36:

touch ${meta.id}.deseq2.results.tsv
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}".deseq2.results.tsv

In .\modules\nf-core\deseq2\differential\main.nf line 37:

touch ${meta.id}.deseq2.dispersion.png
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}".deseq2.dispersion.png

In .\modules\nf-core\deseq2\differential\main.nf line 38:

touch ${meta.id}.dds.rld.rds
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}".dds.rld.rds

In .\modules\nf-core\deseq2\differential\main.nf line 39:

touch ${meta.id}.deseq2.sizefactors.tsv
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}".deseq2.sizefactors.tsv

In .\modules\nf-core\deseq2\differential\main.nf line 40:

touch ${meta.id}.normalised_counts.tsv
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}".normalised_counts.tsv

In .\modules\nf-core\deseq2\differential\main.nf line 41:

touch ${meta.id}.rlog.tsv
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}".rlog.tsv

In .\modules\nf-core\deseq2\differential\main.nf line 42:

touch ${meta.id}.deseq2.model.txt
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}".deseq2.model.txt

In .\modules\nf-core\deseq2\differential\main.nf line 43:

touch ${meta.id}.R_sessionInfo.log
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}".R_sessionInfo.log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\diamond\blastp\main.nf:

In .\modules\nf-core\diamond\blastp\main.nf line 61:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\diamond\blastp\main.nf line 62:

    --db ${db} \
         ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --db "${db}" \

In .\modules\nf-core\diamond\blastp\main.nf line 63:

    --query ${fasta} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --query "${fasta}" \

In .\modules\nf-core\diamond\blastp\main.nf line 64:

    --outfmt ${outfmt} ${columns} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outfmt "${outfmt}" "${columns}" \

In .\modules\nf-core\diamond\blastp\main.nf line 65:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\diamond\blastp\main.nf line 66:

    --out ${prefix}.${out_ext}
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --out "${prefix}"."${out_ext}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\diamond\blastx\main.nf:

In .\modules\nf-core\diamond\blastx\main.nf line 52:

    gzip -c -d ${fasta} > ${fasta_name}
               ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "${fasta}" > "${fasta_name}"

In .\modules\nf-core\diamond\blastx\main.nf line 55:

DB=`find -L ./ -name "*.dmnd" | sed 's/\.dmnd\$//'`
^-- SC2034 (warning): DB appears unused. Verify use (or export if used externally).
   ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
DB=$(find -L ./ -name "*.dmnd" | sed 's/\.dmnd\$//')

In .\modules\nf-core\diamond\blastx\main.nf line 59:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\diamond\blastx\main.nf line 61:

    --query ${fasta_name} \
            ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --query "${fasta_name}" \

In .\modules\nf-core\diamond\blastx\main.nf line 62:

    --outfmt ${outfmt} ${columns} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outfmt "${outfmt}" "${columns}" \

In .\modules\nf-core\diamond\blastx\main.nf line 63:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\diamond\blastx\main.nf line 64:

    --out ${prefix}.${out_ext} \
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --out "${prefix}"."${out_ext}" \

In .\modules\nf-core\diamond\blastx\main.nf line 67:

mv diamond.log ${prefix}.log
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv diamond.log "${prefix}".log

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- DB appears unused. Verify use (or...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\diamond\cluster\main.nf:

In .\modules\nf-core\diamond\cluster\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\diamond\cluster\main.nf line 29:

    $memarg \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$memarg" \

In .\modules\nf-core\diamond\cluster\main.nf line 30:

    -p $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "$task".cpus \

In .\modules\nf-core\diamond\cluster\main.nf line 31:

    -d $db \
       ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -d "$db" \

In .\modules\nf-core\diamond\cluster\main.nf line 32:

    -o ${prefix}.tsv
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\diamond\makedb\main.nf:

In .\modules\nf-core\diamond\makedb\main.nf line 34:

    gzip -c -d ${fasta} > ${fasta_name}
               ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "${fasta}" > "${fasta_name}"

In .\modules\nf-core\diamond\makedb\main.nf line 39:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\diamond\makedb\main.nf line 40:

    --in  ${fasta_name} \
          ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --in  "${fasta_name}" \

In .\modules\nf-core\diamond\makedb\main.nf line 41:

    -d ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -d "${prefix}" \

In .\modules\nf-core\diamond\makedb\main.nf line 42:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\diamond\makedb\main.nf line 43:

    ${insert_taxonmap} \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_taxonmap}" \

In .\modules\nf-core\diamond\makedb\main.nf line 44:

    ${insert_taxonnodes} \
    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_taxonnodes}" \

In .\modules\nf-core\diamond\makedb\main.nf line 45:

    ${insert_taxonnames}
    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${insert_taxonnames}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\doubletdetection\main.nf:

In .\modules\nf-core\doubletdetection\main.nf line 31:

touch ${prefix}.h5ad
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".h5ad

In .\modules\nf-core\doubletdetection\main.nf line 32:

touch ${prefix}.pkl
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".pkl

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dragmap\align\main.nf:

In .\modules\nf-core\dragmap\align\main.nf line 45:

    -r ${hashmap} \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -r "${hashmap}" \

In .\modules\nf-core\dragmap\align\main.nf line 46:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\dragmap\align\main.nf line 47:

    --num-threads ${task.cpus} \
                  ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --num-threads "${task.cpus}" \

In .\modules\nf-core\dragmap\align\main.nf line 48:

    ${reads_command} \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reads_command}" \

In .\modules\nf-core\dragmap\align\main.nf line 49:

    2> >(tee ${prefix}.dragmap.log >&2) \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    2> >(tee "${prefix}".dragmap.log >&2) \

In .\modules\nf-core\dragmap\align\main.nf line 50:

    | samtools ${samtools_command} ${args2} --threads ${task.cpus} ${reference} -o ${prefix}.${extension} -
               ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                   ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                      ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                   ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                             ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | samtools "${samtools_command}" "${args2}" --threads "${task.cpus}" "${reference}" -o "${prefix}"."${extension}" -

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dragmap\hashtable\main.nf:

In .\modules\nf-core\dragmap\hashtable\main.nf line 27:

    --ht-reference ${fasta} \
                   ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ht-reference "${fasta}" \

In .\modules\nf-core\dragmap\hashtable\main.nf line 29:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\dragmap\hashtable\main.nf line 30:

    --ht-num-threads ${task.cpus}
                     ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ht-num-threads "${task.cpus}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dragonflye\main.nf:

In .\modules\nf-core\dragonflye\main.nf line 31:

    --reads ${longreads} \
            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reads "${longreads}" \

In .\modules\nf-core\dragonflye\main.nf line 32:

    $shortreads_polishing \
    ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$shortreads_polishing" \

In .\modules\nf-core\dragonflye\main.nf line 33:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\dragonflye\main.nf line 34:

    --prefix ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --prefix "${prefix}" \

In .\modules\nf-core\dragonflye\main.nf line 35:

    --cpus $task.cpus \
           ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpus "$task".cpus \

In .\modules\nf-core\dragonflye\main.nf line 36:

    --ram $memory \
          ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ram "$memory" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\drep\compare\main.nf:

In .\modules\nf-core\drep\compare\main.nf line 26:

    ${prefix} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}" \

In .\modules\nf-core\drep\compare\main.nf line 27:

    -p ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${task.cpus}" \

In .\modules\nf-core\drep\compare\main.nf line 28:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dshbio\exportsegments\main.nf:

In .\modules\nf-core\dshbio\exportsegments\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\dshbio\exportsegments\main.nf line 27:

    -i $gfa \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$gfa" \

In .\modules\nf-core\dshbio\exportsegments\main.nf line 28:

    -o ${prefix}.fa.gz
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".fa.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dshbio\filterbed\main.nf:

In .\modules\nf-core\dshbio\filterbed\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\dshbio\filterbed\main.nf line 27:

    -i $bed \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bed" \

In .\modules\nf-core\dshbio\filterbed\main.nf line 28:

    -o ${prefix}.bed.gz
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".bed.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dshbio\filtergff3\main.nf:

In .\modules\nf-core\dshbio\filtergff3\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\dshbio\filtergff3\main.nf line 27:

    -i $gff3 \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$gff3" \

In .\modules\nf-core\dshbio\filtergff3\main.nf line 28:

    -o ${prefix}.gff3.gz
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".gff3.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dshbio\splitbed\main.nf:

In .\modules\nf-core\dshbio\splitbed\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\dshbio\splitbed\main.nf line 27:

    -p $prefix \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "$prefix" \

In .\modules\nf-core\dshbio\splitbed\main.nf line 29:

    -i $bed
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bed"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dshbio\splitgff3\main.nf:

In .\modules\nf-core\dshbio\splitgff3\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\dshbio\splitgff3\main.nf line 27:

    -p $prefix \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "$prefix" \

In .\modules\nf-core\dshbio\splitgff3\main.nf line 29:

    -i $gff3
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$gff3"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\duphold\main.nf:

In .\modules\nf-core\duphold\main.nf line 30:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\duphold\main.nf line 31:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\duphold\main.nf line 32:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\duphold\main.nf line 33:

    --vcf ${sv_variants} \
          ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --vcf "${sv_variants}" \

In .\modules\nf-core\duphold\main.nf line 34:

    --bam ${alignment_file} \
          ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bam "${alignment_file}" \

In .\modules\nf-core\duphold\main.nf line 35:

    --fasta ${fasta} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fasta "${fasta}" \

In .\modules\nf-core\duphold\main.nf line 36:

    ${snp_annotation}
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${snp_annotation}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dupradar\main.nf:

In .\modules\nf-core\dupradar\main.nf line 32:

touch ${meta.id}_duprateExpDens.pdf
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}"_duprateExpDens.pdf

In .\modules\nf-core\dupradar\main.nf line 33:

touch ${meta.id}_duprateExpBoxplot.pdf
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}"_duprateExpBoxplot.pdf

In .\modules\nf-core\dupradar\main.nf line 34:

touch ${meta.id}_expressionHist.pdf
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}"_expressionHist.pdf

In .\modules\nf-core\dupradar\main.nf line 35:

touch ${meta.id}_dupMatrix.txt
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}"_dupMatrix.txt

In .\modules\nf-core\dupradar\main.nf line 36:

touch ${meta.id}_intercept_slope.txt
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}"_intercept_slope.txt

In .\modules\nf-core\dupradar\main.nf line 37:

touch ${meta.id}_dup_intercept_mqc.txt
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}"_dup_intercept_mqc.txt

In .\modules\nf-core\dupradar\main.nf line 38:

touch ${meta.id}_duprateExpDensCurve_mqc.txt
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}"_duprateExpDensCurve_mqc.txt

In .\modules\nf-core\dupradar\main.nf line 39:

touch ${meta.id}.R_sessionInfo.log
      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${meta.id}".R_sessionInfo.log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\dysgu\main.nf:

In .\modules\nf-core\dysgu\main.nf line 29:

    -p ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${task.cpus}" \

In .\modules\nf-core\dysgu\main.nf line 31:

    $fasta \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" \

In .\modules\nf-core\dysgu\main.nf line 33:

    $input \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" \

In .\modules\nf-core\dysgu\main.nf line 34:

    | bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                               ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | bgzip "${args2}" --threads "${task.cpus}" --stdout > "${prefix}".vcf.gz

In .\modules\nf-core\dysgu\main.nf line 35:

tabix ${args3} ${prefix}.vcf.gz
      ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
tabix "${args3}" "${prefix}".vcf.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\eagle2\main.nf:

In .\modules\nf-core\eagle2\main.nf line 27:

    $input_cmd \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_cmd" \

In .\modules\nf-core\eagle2\main.nf line 28:

    $vcfref_cmd \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcfref_cmd" \

In .\modules\nf-core\eagle2\main.nf line 29:

    --geneticMapFile $map \
                     ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --geneticMapFile "$map" \

In .\modules\nf-core\eagle2\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\eagle2\main.nf line 31:

    --numThreads $task.cpus \
                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --numThreads "$task".cpus \

In .\modules\nf-core\eagle2\main.nf line 32:

    --outPrefix ${prefix} \
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outPrefix "${prefix}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ectyper\main.nf:

In .\modules\nf-core\ectyper\main.nf line 29:

    gzip -c -d $fasta > $fasta_name
               ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "$fasta" > "$fasta_name"

In .\modules\nf-core\ectyper\main.nf line 33:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ectyper\main.nf line 34:

    --cores $task.cpus \
            ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cores "$task".cpus \

In .\modules\nf-core\ectyper\main.nf line 36:

    --input $fasta_name
            ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$fasta_name"

In .\modules\nf-core\ectyper\main.nf line 38:

mv output.tsv ${prefix}.tsv
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv output.tsv "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\eggnogmapper\main.nf:

In .\modules\nf-core\eggnogmapper\main.nf line 35:

    gzip -c -d $fasta > $fasta_name
               ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "$fasta" > "$fasta_name"

In .\modules\nf-core\eggnogmapper\main.nf line 39:

    --cpu ${task.cpus} \
          ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpu "${task.cpus}" \

In .\modules\nf-core\eggnogmapper\main.nf line 40:

    -i ${fasta_name} \
       ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${fasta_name}" \

In .\modules\nf-core\eggnogmapper\main.nf line 41:

    --data_dir ${eggnog_data_dir} \
               ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --data_dir "${eggnog_data_dir}" \

In .\modules\nf-core\eggnogmapper\main.nf line 43:

    $dmnd_db_arg \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$dmnd_db_arg" \

In .\modules\nf-core\eggnogmapper\main.nf line 44:

    $database_arg \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$database_arg" \

In .\modules\nf-core\eggnogmapper\main.nf line 45:

    --output ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}" \

In .\modules\nf-core\eggnogmapper\main.nf line 46:

    ${dbmem} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${dbmem}" \

In .\modules\nf-core\eggnogmapper\main.nf line 47:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\eido\convert\main.nf:

In .\modules\nf-core\eido\convert\main.nf line 28:

    -f $format \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -f "$format" \

In .\modules\nf-core\eido\convert\main.nf line 29:

    $samplesheet \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$samplesheet" \

In .\modules\nf-core\eido\convert\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\eido\convert\main.nf line 31:

    -p samples=${prefix}.${format}
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p samples="${prefix}"."${format}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\eido\validate\main.nf:

In .\modules\nf-core\eido\validate\main.nf line 26:

eido validate $args $samplesheet -s $schema -e > ${prefix}.log
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
eido validate "$args" "$samplesheet" -s "$schema" -e > "${prefix}".log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\eigenstratdatabasetools\eigenstratsnpcoverage\main.nf:

In .\modules\nf-core\eigenstratdatabasetools\eigenstratsnpcoverage\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\eigenstratdatabasetools\eigenstratsnpcoverage\main.nf line 27:

    -g ${geno} \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "${geno}" \

In .\modules\nf-core\eigenstratdatabasetools\eigenstratsnpcoverage\main.nf line 28:

    -s ${snp} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -s "${snp}" \

In .\modules\nf-core\eigenstratdatabasetools\eigenstratsnpcoverage\main.nf line 29:

    -i ${ind} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${ind}" \

In .\modules\nf-core\eigenstratdatabasetools\eigenstratsnpcoverage\main.nf line 30:

    -o ${prefix}.tsv
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\eklipse\main.nf:

In .\modules\nf-core\eklipse\main.nf line 31:

echo "$bam\t${prefix}" > infile.txt
     ^---------------^ SC2028 (info): echo may not expand escape sequences. Use printf.

In .\modules\nf-core\eklipse\main.nf line 34:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\eklipse\main.nf line 35:

    -ref $ref_gb
         ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -ref "$ref_gb"

In .\modules\nf-core\eklipse\main.nf line 36:

mv eKLIPse_*/eKLIPse_deletions.csv eKLIPse_${prefix}_deletions.csv
                                           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv eKLIPse_*/eKLIPse_deletions.csv eKLIPse_"${prefix}"_deletions.csv

In .\modules\nf-core\eklipse\main.nf line 37:

mv eKLIPse_*/eKLIPse_genes.csv eKLIPse_${prefix}_genes.csv
                                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv eKLIPse_*/eKLIPse_genes.csv eKLIPse_"${prefix}"_genes.csv

In .\modules\nf-core\eklipse\main.nf line 38:

mv eKLIPse_*/eKLIPse_${prefix}.png eKLIPse_${prefix}.png
                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv eKLIPse_*/eKLIPse_"${prefix}".png eKLIPse_"${prefix}".png

For more information:
  https://www.shellcheck.net/wiki/SC2028 -- echo may not expand escape sequen...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\elprep\fastatoelfasta\main.nf:

In .\modules\nf-core\elprep\fastatoelfasta\main.nf line 25:

    $fasta \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" \

In .\modules\nf-core\elprep\fastatoelfasta\main.nf line 26:

    ${prefix}.elfasta \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".elfasta \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\elprep\filter\main.nf:

In .\modules\nf-core\elprep\filter\main.nf line 68:

elprep filter ${bam} ${prefix}.${suffix} \
              ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
elprep filter "${bam}" "${prefix}"."${suffix}" \

In .\modules\nf-core\elprep\filter\main.nf line 69:

    ${reference_sequences_cmd} \
    ^------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reference_sequences_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 70:

    ${filter_regions_cmd} \
    ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${filter_regions_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 71:

    ${markdup_cmd} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${markdup_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 72:

    ${haplotyper_cmd} \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${haplotyper_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 73:

    ${fasta_cmd} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fasta_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 74:

    ${known_sites_cmd} \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${known_sites_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 75:

    ${target_regions_cmd} \
    ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${target_regions_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 76:

    ${bqsr_cmd} \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bqsr_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 77:

    ${bqsr_tables_only_cmd} \
    ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bqsr_tables_only_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 78:

    ${intermediate_bqsr_cmd} \
    ^----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${intermediate_bqsr_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 79:

    ${input_recall_cmd} \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_recall_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 80:

    ${activity_profile_cmd} \
    ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${activity_profile_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 81:

    ${assembly_regions_cmd} \
    ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${assembly_regions_cmd}" \

In .\modules\nf-core\elprep\filter\main.nf line 82:

    --nr-of-threads ${task.cpus} \
                    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nr-of-threads "${task.cpus}" \

In .\modules\nf-core\elprep\filter\main.nf line 84:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\elprep\merge\main.nf:

In .\modules\nf-core\elprep\merge\main.nf line 29:

mv ${bam} input/
   ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${bam}" input/

In .\modules\nf-core\elprep\merge\main.nf line 33:

    output/${prefix}.${suffix} \
           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    output/"${prefix}"."${suffix}" \

In .\modules\nf-core\elprep\merge\main.nf line 34:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\elprep\merge\main.nf line 35:

    ${single_end} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${single_end}" \

In .\modules\nf-core\elprep\merge\main.nf line 37:

    --nr-of-threads $task.cpus
                    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nr-of-threads "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\elprep\split\main.nf:

In .\modules\nf-core\elprep\split\main.nf line 28:

mv ${bam} input/
   ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${bam}" input/

In .\modules\nf-core\elprep\split\main.nf line 30:

mkdir ${prefix}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mkdir "${prefix}"

In .\modules\nf-core\elprep\split\main.nf line 36:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\elprep\split\main.nf line 37:

    $single_end \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$single_end" \

In .\modules\nf-core\elprep\split\main.nf line 38:

    --nr-of-threads $task.cpus \
                    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nr-of-threads "$task".cpus \

In .\modules\nf-core\elprep\split\main.nf line 40:

    --output-prefix $prefix
                    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-prefix "$prefix"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\emboss\cons\main.nf:

In .\modules\nf-core\emboss\cons\main.nf line 26:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\emboss\cons\main.nf line 27:

    -name ${prefix} \
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -name "${prefix}" \

In .\modules\nf-core\emboss\cons\main.nf line 28:

    -sequence $fasta \
              ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -sequence "$fasta" \

In .\modules\nf-core\emboss\cons\main.nf line 29:

    -outseq ${prefix}.fa \
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -outseq "${prefix}".fa \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\emboss\revseq\main.nf:

In .\modules\nf-core\emboss\revseq\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\emboss\revseq\main.nf line 28:

    $sequences \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sequences" \

In .\modules\nf-core\emboss\revseq\main.nf line 29:

    $outfile
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$outfile"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\emboss\seqret\main.nf:

In .\modules\nf-core\emboss\seqret\main.nf line 27:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\emboss\seqret\main.nf line 28:

    -sequence ${sequence} \
              ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -sequence "${sequence}" \

In .\modules\nf-core\emboss\seqret\main.nf line 29:

    ${osformat} \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${osformat}" \

In .\modules\nf-core\emboss\seqret\main.nf line 30:

    -outseq ${prefix}.${out_ext}
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -outseq "${prefix}"."${out_ext}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\emmtyper\main.nf:

In .\modules\nf-core\emmtyper\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\emmtyper\main.nf line 26:

    $fasta \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" \

In .\modules\nf-core\emmtyper\main.nf line 27:

    > ${prefix}.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\emu\abundance\main.nf:

In .\modules\nf-core\emu\abundance\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\emu\abundance\main.nf line 32:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\emu\abundance\main.nf line 33:

    --db $db \
         ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --db "$db" \

In .\modules\nf-core\emu\abundance\main.nf line 34:

    $reads
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\endorspy\main.nf:

In .\modules\nf-core\endorspy\main.nf line 31:

    $optionalraw \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$optionalraw" \

In .\modules\nf-core\endorspy\main.nf line 32:

    $optionalqualityfiltered \
    ^----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$optionalqualityfiltered" \

In .\modules\nf-core\endorspy\main.nf line 33:

    $optionaldeduplicated \
    ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$optionaldeduplicated" \

In .\modules\nf-core\endorspy\main.nf line 34:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\endorspy\main.nf line 36:

    -n $prefix
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -n "$prefix"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ensemblvep\download\main.nf:

In .\modules\nf-core\ensemblvep\download\main.nf line 25:

    --CACHEDIR $prefix \
               ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --CACHEDIR "$prefix" \

In .\modules\nf-core\ensemblvep\download\main.nf line 26:

    --SPECIES $species \
              ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --SPECIES "$species" \

In .\modules\nf-core\ensemblvep\download\main.nf line 27:

    --ASSEMBLY $assembly \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ASSEMBLY "$assembly" \

In .\modules\nf-core\ensemblvep\download\main.nf line 28:

    --CACHE_VERSION $cache_version \
                    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --CACHE_VERSION "$cache_version" \

In .\modules\nf-core\ensemblvep\download\main.nf line 29:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ensemblvep\filtervep\main.nf:

In .\modules\nf-core\ensemblvep\filtervep\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ensemblvep\filtervep\main.nf line 28:

    --input_file $input \
                 ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input_file "$input" \

In .\modules\nf-core\ensemblvep\filtervep\main.nf line 29:

    --output_file ${prefix}.${extension} \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output_file "${prefix}"."${extension}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ensemblvep\vep\main.nf:

In .\modules\nf-core\ensemblvep\vep\main.nf line 41:

    -i $vcf \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$vcf" \

In .\modules\nf-core\ensemblvep\vep\main.nf line 42:

    -o ${prefix}.${file_extension}.gz \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                 ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}"."${file_extension}".gz \

In .\modules\nf-core\ensemblvep\vep\main.nf line 43:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ensemblvep\vep\main.nf line 44:

    $compress_cmd \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$compress_cmd" \

In .\modules\nf-core\ensemblvep\vep\main.nf line 45:

    $reference \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference" \

In .\modules\nf-core\ensemblvep\vep\main.nf line 46:

    --assembly $genome \
               ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --assembly "$genome" \

In .\modules\nf-core\ensemblvep\vep\main.nf line 47:

    --species $species \
              ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --species "$species" \

In .\modules\nf-core\ensemblvep\vep\main.nf line 49:

    --cache_version $cache_version \
                    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cache_version "$cache_version" \

In .\modules\nf-core\ensemblvep\vep\main.nf line 50:

    --dir_cache $dir_cache \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --dir_cache "$dir_cache" \

In .\modules\nf-core\ensemblvep\vep\main.nf line 51:

    --fork $task.cpus
           ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fork "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\entrezdirect\esearch\main.nf:

In .\modules\nf-core\entrezdirect\esearch\main.nf line 26:

    -db $database \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -db "$database" \

In .\modules\nf-core\entrezdirect\esearch\main.nf line 27:

    -query $term \
           ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -query "$term" \

In .\modules\nf-core\entrezdirect\esearch\main.nf line 28:

    $args > ${prefix}.xml
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" > "${prefix}".xml

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\entrezdirect\esummary\main.nf:

In .\modules\nf-core\entrezdirect\esummary\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\entrezdirect\esummary\main.nf line 30:

    -db $database \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -db "$database" \

In .\modules\nf-core\entrezdirect\esummary\main.nf line 31:

    $input > ${prefix}.xml
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" > "${prefix}".xml

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\entrezdirect\xtract\main.nf:

In .\modules\nf-core\entrezdirect\xtract\main.nf line 27:

cat $xml_input | xtract \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
cat "$xml_input" | xtract \

In .\modules\nf-core\entrezdirect\xtract\main.nf line 28:

    -pattern $pattern \
             ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -pattern "$pattern" \

In .\modules\nf-core\entrezdirect\xtract\main.nf line 29:

    -tab $sep \
         ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -tab "$sep" \

In .\modules\nf-core\entrezdirect\xtract\main.nf line 30:

    -element $element \
             ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -element "$element" \

In .\modules\nf-core\entrezdirect\xtract\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\entrezdirect\xtract\main.nf line 32:

    > ${prefix}.txt
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\epang\place\main.nf:

In .\modules\nf-core\epang\place\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\epang\place\main.nf line 36:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\epang\place\main.nf line 37:

    $queryarg \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$queryarg" \

In .\modules\nf-core\epang\place\main.nf line 38:

    $refalnarg \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$refalnarg" \

In .\modules\nf-core\epang\place\main.nf line 39:

    $reftreearg \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reftreearg" \

In .\modules\nf-core\epang\place\main.nf line 40:

    $bfastarg \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bfastarg" \

In .\modules\nf-core\epang\place\main.nf line 41:

    $binaryarg
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$binaryarg"

In .\modules\nf-core\epang\place\main.nf line 45:

    cp epa_result.jplace.gz ${prefix}.epa_result.jplace.gz
                            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    cp epa_result.jplace.gz "${prefix}".epa_result.jplace.gz

In .\modules\nf-core\epang\place\main.nf line 47:

[ -e epa_info.log ]      && cp epa_info.log ${prefix}.epa_info.log
                                            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
[ -e epa_info.log ]      && cp epa_info.log "${prefix}".epa_info.log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\epang\split\main.nf:

In .\modules\nf-core\epang\split\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\epang\split\main.nf line 27:

    --split $refaln $fullaln
            ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --split "$refaln" "$fullaln"

In .\modules\nf-core\epang\split\main.nf line 29:

gzip -c query.fasta > ${prefix}.query.fasta.gz; rm query.fasta
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip -c query.fasta > "${prefix}".query.fasta.gz; rm query.fasta

In .\modules\nf-core\epang\split\main.nf line 30:

gzip -c reference.fasta > ${prefix}.reference.fasta.gz; rm reference.fasta
                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip -c reference.fasta > "${prefix}".reference.fasta.gz; rm reference.fasta

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\estsfs\main.nf:

In .\modules\nf-core\estsfs\main.nf line 27:

est-sfs ${e_config} ${data} ${seed} ${prefix}_sfs.txt ${prefix}_pvalues.txt
        ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                            ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
est-sfs "${e_config}" "${data}" "${seed}" "${prefix}"_sfs.txt "${prefix}"_pvalues.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\evigene\tr2aacds\main.nf:

In .\modules\nf-core\evigene\tr2aacds\main.nf line 39:

    . "/usr/local/env-activate.sh"
      ^--------------------------^ SC1091 (info): Not following: /usr/local/env-activate.sh was not specified as input (see shellcheck -x).

In .\modules\nf-core\evigene\tr2aacds\main.nf line 44:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\evigene\tr2aacds\main.nf line 45:

    -NCPU=$task.cpus \
          ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -NCPU="$task".cpus \

In .\modules\nf-core\evigene\tr2aacds\main.nf line 46:

    -MAXMEM=$max_memory \
            ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -MAXMEM="$max_memory" \

In .\modules\nf-core\evigene\tr2aacds\main.nf line 47:

    -cdnaseq $fasta
             ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -cdnaseq "$fasta"

For more information:
  https://www.shellcheck.net/wiki/SC1091 -- Not following: /usr/local/env-act...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\expansionhunter\main.nf:

In .\modules\nf-core\expansionhunter\main.nf line 32:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\expansionhunter\main.nf line 33:

    --reads ${bam} \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reads "${bam}" \

In .\modules\nf-core\expansionhunter\main.nf line 34:

    --output-prefix ${prefix} \
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-prefix "${prefix}" \

In .\modules\nf-core\expansionhunter\main.nf line 35:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\expansionhunter\main.nf line 36:

    --variant-catalog ${variant_catalog}
                      ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant-catalog "${variant_catalog}"

In .\modules\nf-core\expansionhunter\main.nf line 38:

bgzip --threads ${task.cpus} ${args2} ${prefix}.vcf
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                             ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bgzip --threads "${task.cpus}" "${args2}" "${prefix}".vcf

In .\modules\nf-core\expansionhunter\main.nf line 39:

bgzip --threads ${task.cpus} ${args2} ${prefix}.json
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                             ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bgzip --threads "${task.cpus}" "${args2}" "${prefix}".json

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\expansionhunterdenovo\merge\main.nf:

In .\modules\nf-core\expansionhunterdenovo\merge\main.nf line 28:

    --manifest ${manifest} \
               ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --manifest "${manifest}" \

In .\modules\nf-core\expansionhunterdenovo\merge\main.nf line 29:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\expansionhunterdenovo\merge\main.nf line 30:

    --output-prefix ${prefix} \
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-prefix "${prefix}" \

In .\modules\nf-core\expansionhunterdenovo\merge\main.nf line 31:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\expansionhunterdenovo\profile\main.nf:

In .\modules\nf-core\expansionhunterdenovo\profile\main.nf line 30:

    --reads ${alignment_file} \
            ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reads "${alignment_file}" \

In .\modules\nf-core\expansionhunterdenovo\profile\main.nf line 31:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\expansionhunterdenovo\profile\main.nf line 32:

    --output-prefix ${prefix} \
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-prefix "${prefix}" \

In .\modules\nf-core\expansionhunterdenovo\profile\main.nf line 33:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\falco\main.nf:

In .\modules\nf-core\falco\main.nf line 27:

falco $args --threads $task.cpus ${reads} -D ${prefix}_fastqc_data.txt -S ${prefix}_summary.txt -R ${prefix}_report.html
      ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                      ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
falco "$args" --threads "$task".cpus "${reads}" -D "${prefix}"_fastqc_data.txt -S "${prefix}"_summary.txt -R "${prefix}"_report.html

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\famsa\align\main.nf:

In .\modules\nf-core\famsa\align\main.nf line 30:

famsa $options_tree \
      ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
famsa "$options_tree" \

In .\modules\nf-core\famsa\align\main.nf line 31:

    $compress_args \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$compress_args" \

In .\modules\nf-core\famsa\align\main.nf line 32:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\famsa\align\main.nf line 33:

    -t ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "${task.cpus}" \

In .\modules\nf-core\famsa\align\main.nf line 34:

    ${fasta} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fasta}" \

In .\modules\nf-core\famsa\align\main.nf line 35:

    ${prefix}.aln${compress ? '.gz':''}
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                 ^--------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".aln"${compress ? '.gz':''}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\famsa\guidetree\main.nf:

In .\modules\nf-core\famsa\guidetree\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\famsa\guidetree\main.nf line 27:

    -t ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "${task.cpus}" \

In .\modules\nf-core\famsa\guidetree\main.nf line 28:

    ${fasta} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fasta}" \

In .\modules\nf-core\famsa\guidetree\main.nf line 29:

    ${prefix}.dnd
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".dnd

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\faqcs\main.nf:

In .\modules\nf-core\faqcs\main.nf line 32:

[ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                      ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
[ ! -f  "${prefix}".fastq.gz ] && ln -s "$reads" "${prefix}".fastq.gz

In .\modules\nf-core\faqcs\main.nf line 35:

    -u ${prefix}.fastq.gz \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -u "${prefix}".fastq.gz \

In .\modules\nf-core\faqcs\main.nf line 36:

    --prefix ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --prefix "${prefix}" \

In .\modules\nf-core\faqcs\main.nf line 37:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\faqcs\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\faqcs\main.nf line 39:

    2> >(tee ${prefix}.log >&2)
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    2> >(tee "${prefix}".log >&2)

In .\modules\nf-core\faqcs\main.nf line 43:

    mv ${prefix}.unpaired.trimmed.fastq ${prefix}.trimmed.fastq
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    mv "${prefix}".unpaired.trimmed.fastq "${prefix}".trimmed.fastq

In .\modules\nf-core\faqcs\main.nf line 44:

    gzip ${prefix}.trimmed.fastq
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip "${prefix}".trimmed.fastq

In .\modules\nf-core\faqcs\main.nf line 47:

    mv ${prefix}.discard.trimmed.fastq ${prefix}.trimmed.discard.fastq
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    mv "${prefix}".discard.trimmed.fastq "${prefix}".trimmed.discard.fastq

In .\modules\nf-core\faqcs\main.nf line 48:

    gzip ${prefix}.trimmed.discard.fastq
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip "${prefix}".trimmed.discard.fastq

In .\modules\nf-core\faqcs\main.nf line 54:

    mv *.{base,for_qual_histogram,length_count,quality}*.* debug
       ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fargene\main.nf:

In .\modules\nf-core\fargene\main.nf line 43:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fargene\main.nf line 44:

    -p $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "$task".cpus \

In .\modules\nf-core\fargene\main.nf line 45:

    -i $input \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$input" \

In .\modules\nf-core\fargene\main.nf line 46:

    --hmm-model $hmm_model \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --hmm-model "$hmm_model" \

In .\modules\nf-core\fargene\main.nf line 47:

    -o $prefix
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "$prefix"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fast2q\main.nf:

In .\modules\nf-core\fast2q\main.nf line 37:

    --fn ${prefix} \
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fn "${prefix}" \

In .\modules\nf-core\fast2q\main.nf line 38:

    --cp ${task.cpus} \
         ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cp "${task.cpus}" \

In .\modules\nf-core\fast2q\main.nf line 39:

    $input_file \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_file" \

In .\modules\nf-core\fast2q\main.nf line 40:

    $library_file \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$library_file" \

In .\modules\nf-core\fast2q\main.nf line 41:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

In .\modules\nf-core\fast2q\main.nf line 43:

mv **/${prefix}* .
   ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv **/"${prefix}"* .

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fastani\main.nf:

In .\modules\nf-core\fastani\main.nf line 28:

    -ql $query \
        ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -ql "$query" \

In .\modules\nf-core\fastani\main.nf line 29:

    -rl $reference \
        ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -rl "$reference" \

In .\modules\nf-core\fastani\main.nf line 30:

    -o ${prefix}.ani.txt
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".ani.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fastavalidator\main.nf:

In .\modules\nf-core\fastavalidator\main.nf line 29:

if [ \$(cat "${prefix}.error.log" | wc -l) -gt 0 ]; then
^-- SC1009 (info): The mentioned syntax error was in this if expression.
   ^-- SC1073 (error): Couldn't parse this test expression. Fix to allow more checks.
       ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
       ^-- SC1072 (error): Expected test to end here (don't wrap commands in []/[[]]). Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1072 -- Expected test to end here (don't ...
  https://www.shellcheck.net/wiki/SC1073 -- Couldn't parse this test expressi...

ShellCheck results for .\modules\nf-core\fastawindows\main.nf:

In .\modules\nf-core\fastawindows\main.nf line 29:

env RAYON_NUM_THREADS=$task.cpus \
                      ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
env RAYON_NUM_THREADS="$task".cpus \

In .\modules\nf-core\fastawindows\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fastawindows\main.nf line 32:

    --fasta $fasta \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fasta "$fasta" \

In .\modules\nf-core\fastawindows\main.nf line 33:

    --output ${prefix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fastk\fastk\main.nf:

In .\modules\nf-core\fastk\fastk\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fastk\fastk\main.nf line 30:

    -T$task.cpus \
      ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -T"$task".cpus \

In .\modules\nf-core\fastk\fastk\main.nf line 31:

    -M${task.memory.toGiga()} \
      ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -M"${task.memory.toGiga()}" \

In .\modules\nf-core\fastk\fastk\main.nf line 32:

    -N${prefix}_fk \
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -N"${prefix}"_fk \

In .\modules\nf-core\fastk\fastk\main.nf line 33:

    $reads
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fastk\histex\main.nf:

In .\modules\nf-core\fastk\histex\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fastk\histex\main.nf line 28:

    $histogram \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$histogram" \

In .\modules\nf-core\fastk\histex\main.nf line 29:

    > ${prefix}.hist
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".hist

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fastk\merge\main.nf:

In .\modules\nf-core\fastk\merge\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fastk\merge\main.nf line 30:

    -T$task.cpus \
      ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -T"$task".cpus \

In .\modules\nf-core\fastk\merge\main.nf line 31:

    ${prefix} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}" \

In .\modules\nf-core\fastk\merge\main.nf line 32:

    $hist
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$hist"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fastme\main.nf:

In .\modules\nf-core\fastme\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fastme\main.nf line 32:

    -i $infile \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$infile" \

In .\modules\nf-core\fastme\main.nf line 33:

    $initarg \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$initarg" \

In .\modules\nf-core\fastme\main.nf line 34:

    -o ${prefix}.nwk \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".nwk \

In .\modules\nf-core\fastme\main.nf line 35:

    $matarg \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$matarg" \

In .\modules\nf-core\fastme\main.nf line 36:

    $bootarg \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bootarg" \

In .\modules\nf-core\fastme\main.nf line 37:

    -T $task.cpus
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -T "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fastp\main.nf:

In .\modules\nf-core\fastp\main.nf line 40:

[ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
[ ! -f  "${prefix}".fastq.gz ] && ln -sf "$reads" "${prefix}".fastq.gz

In .\modules\nf-core\fastp\main.nf line 44:

    --in1 ${prefix}.fastq.gz \
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --in1 "${prefix}".fastq.gz \

In .\modules\nf-core\fastp\main.nf line 45:

    --thread $task.cpus \
             ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --thread "$task".cpus \

In .\modules\nf-core\fastp\main.nf line 46:

    --json ${prefix}.fastp.json \
           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --json "${prefix}".fastp.json \

In .\modules\nf-core\fastp\main.nf line 47:

    --html ${prefix}.fastp.html \
           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --html "${prefix}".fastp.html \

In .\modules\nf-core\fastp\main.nf line 48:

    $adapter_list \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$adapter_list" \

In .\modules\nf-core\fastp\main.nf line 49:

    $fail_fastq \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fail_fastq" \

In .\modules\nf-core\fastp\main.nf line 50:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fastp\main.nf line 51:

    2> >(tee ${prefix}.fastp.log >&2) \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    2> >(tee "${prefix}".fastp.log >&2) \

In .\modules\nf-core\fastp\main.nf line 52:

| gzip -c > ${prefix}.fastp.fastq.gz
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
| gzip -c > "${prefix}".fastp.fastq.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fastqc\main.nf:

In .\modules\nf-core\fastqc\main.nf line 37:

printf "%s %s\n" ${rename_to} | while read old_name new_name; do
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                      ^--^ SC2162 (info): read without -r will mangle backslashes.
                                           ^------^ SC2034 (warning): old_name appears unused. Verify use (or export if used externally).
                                                    ^------^ SC2034 (warning): new_name appears unused. Verify use (or export if used externally).

Did you mean: 
printf "%s %s\n" "${rename_to}" | while read old_name new_name; do

In .\modules\nf-core\fastqc\main.nf line 42:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\fastqc\main.nf line 43:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\fastqc\main.nf line 44:

    --memory ${fastqc_memory} \
             ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --memory "${fastqc_memory}" \

In .\modules\nf-core\fastqc\main.nf line 45:

    ${renamed_files}
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${renamed_files}"

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- new_name appears unused. Verify u...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2162 -- read without -r will mangle backs...

ShellCheck results for .\modules\nf-core\fastqe\main.nf:

In .\modules\nf-core\fastqe\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fastqe\main.nf line 27:

    $fastq \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fastq" \

In .\modules\nf-core\fastqe\main.nf line 28:

    --output ${prefix}.tsv
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fastqscan\main.nf:

In .\modules\nf-core\fastqscan\main.nf line 24:

zcat $reads | \
     ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
zcat "$reads" | \

In .\modules\nf-core\fastqscan\main.nf line 26:

    $args > ${prefix}.json
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" > "${prefix}".json

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fastqscreen\buildfromindex\main.nf:

In .\modules\nf-core\fastqscreen\buildfromindex\main.nf line 40:

for f in ${folder.join(' ')}
^-- SC1073 (error): Couldn't parse this for loop. Fix to allow more checks.

In .\modules\nf-core\fastqscreen\buildfromindex\main.nf line 41:

do
^-- SC1061 (error): Couldn't find 'done' for this 'do'.

In .\modules\nf-core\fastqscreen\buildfromindex\main.nf line 42:

    TO_REPLACE=\${f}_to_be_replaced
                 ^-- SC1083 (warning): This { is literal. Check expression (missing ;/\n?) or quote it.
                   ^-- SC1083 (warning): This } is literal. Check expression (missing ;/\n?) or quote it.

In .\modules\nf-core\fastqscreen\buildfromindex\main.nf line 45:

    REPLACE_WITH=\$(basename \$REPLACE_WITH)
                   ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
                   ^-- SC1062 (error): Expected 'done' matching previously mentioned 'do'.
                   ^-- SC1072 (error): Expected 'done'. Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1061 -- Couldn't find 'done' for this 'do'.
  https://www.shellcheck.net/wiki/SC1083 -- This { is literal. Check expressi...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...

ShellCheck results for .\modules\nf-core\fastqscreen\fastqscreen\main.nf:

In .\modules\nf-core\fastqscreen\fastqscreen\main.nf line 29:

fastq_screen --threads ${task.cpus} \
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
fastq_screen --threads "${task.cpus}" \

In .\modules\nf-core\fastqscreen\fastqscreen\main.nf line 31:

    --conf ${database}/fastq_screen.conf \
           ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --conf "${database}"/fastq_screen.conf \

In .\modules\nf-core\fastqscreen\fastqscreen\main.nf line 32:

    $reads \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads" \

In .\modules\nf-core\fastqscreen\fastqscreen\main.nf line 33:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fasttree\main.nf:

In .\modules\nf-core\fasttree\main.nf line 23:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fasttree\main.nf line 25:

    -nt $alignment \
        ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -nt "$alignment" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fastx\collapser\main.nf:

In .\modules\nf-core\fastx\collapser\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fastx\collapser\main.nf line 26:

    -i $fastx \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$fastx" \

In .\modules\nf-core\fastx\collapser\main.nf line 27:

    -o ${prefix}.fasta
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".fasta

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fcs\fcsadaptor\main.nf:

In .\modules\nf-core\fcs\fcsadaptor\main.nf line 48:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fcs\fcsadaptor\main.nf line 49:

    $assembly
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$assembly"

In .\modules\nf-core\fcs\fcsadaptor\main.nf line 52:

num_contamination_lines=\$(cat "output/fcs_adaptor_report.txt" | wc -l)
^---------------------^ SC2034 (warning): num_contamination_lines appears unused. Verify use (or export if used externally).
                          ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
                          ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- num_contamination_lines appears u...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...

ShellCheck results for .\modules\nf-core\fcs\fcsgx\main.nf:

In .\modules\nf-core\fcs\fcsgx\main.nf line 42:

    --fasta $assembly \
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fasta "$assembly" \

In .\modules\nf-core\fcs\fcsgx\main.nf line 44:

    --gx-db ./${gxdb[0].baseName} \
              ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gx-db ./"${gxdb[0].baseName}" \

In .\modules\nf-core\fcs\fcsgx\main.nf line 45:

    --tax-id ${meta.taxid} \
             ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --tax-id "${meta.taxid}" \

In .\modules\nf-core\fcs\fcsgx\main.nf line 46:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fcsgx\cleangenome\main.nf:

In .\modules\nf-core\fcsgx\cleangenome\main.nf line 27:

    --input ${fasta} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${fasta}" \

In .\modules\nf-core\fcsgx\cleangenome\main.nf line 28:

    --action-report ${fcsgx_report} \
                    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --action-report "${fcsgx_report}" \

In .\modules\nf-core\fcsgx\cleangenome\main.nf line 29:

    --output ${prefix}.cleaned.fasta \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".cleaned.fasta \

In .\modules\nf-core\fcsgx\cleangenome\main.nf line 30:

    --contam-fasta-out ${prefix}.contaminants.fasta \
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --contam-fasta-out "${prefix}".contaminants.fasta \

In .\modules\nf-core\fcsgx\cleangenome\main.nf line 31:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fcsgx\rungx\main.nf:

In .\modules\nf-core\fcsgx\rungx\main.nf line 34:

trap "rm -rf "${database}" EXIT
^-- SC1009 (info): The mentioned syntax error was in this simple command.
                         ^-- SC1073 (error): Couldn't parse this double quoted string. Fix to allow more checks.

In .\modules\nf-core\fcsgx\rungx\main.nf line 36:

^-- SC1072 (error): Expected end of double quoted string. Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1072 -- Expected end of double quoted str...
  https://www.shellcheck.net/wiki/SC1073 -- Couldn't parse this double quoted...
  https://www.shellcheck.net/wiki/SC1009 -- The mentioned syntax error was in...

ShellCheck results for .\modules\nf-core\ffq\main.nf:

In .\modules\nf-core\ffq\main.nf line 27:

    ${id_list.join(' ')} \
    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${id_list.join(' ')}" \

In .\modules\nf-core\ffq\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ffq\main.nf line 29:

    > ${prefix}.json
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".json

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fgbio\callduplexconsensusreads\main.nf:

In .\modules\nf-core\fgbio\callduplexconsensusreads\main.nf line 40:

    -Xmx${mem_gb}g \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${mem_gb}"g \

In .\modules\nf-core\fgbio\callduplexconsensusreads\main.nf line 45:

    --input $grouped_bam \
            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$grouped_bam" \

In .\modules\nf-core\fgbio\callduplexconsensusreads\main.nf line 46:

    --output ${prefix}.bam \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".bam \

In .\modules\nf-core\fgbio\callduplexconsensusreads\main.nf line 47:

    --min-reads ${min_reads} \
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --min-reads "${min_reads}" \

In .\modules\nf-core\fgbio\callduplexconsensusreads\main.nf line 48:

    --min-input-base-quality ${min_baseq} \
                             ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --min-input-base-quality "${min_baseq}" \

In .\modules\nf-core\fgbio\callduplexconsensusreads\main.nf line 49:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\fgbio\callduplexconsensusreads\main.nf line 50:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fgbio\callmolecularconsensusreads\main.nf:

In .\modules\nf-core\fgbio\callmolecularconsensusreads\main.nf line 34:

    -Xmx${mem_gb}g \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${mem_gb}"g \

In .\modules\nf-core\fgbio\callmolecularconsensusreads\main.nf line 39:

    --input $grouped_bam \
            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$grouped_bam" \

In .\modules\nf-core\fgbio\callmolecularconsensusreads\main.nf line 40:

    --output ${prefix}.bam \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".bam \

In .\modules\nf-core\fgbio\callmolecularconsensusreads\main.nf line 41:

    --min-reads ${min_reads} \
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --min-reads "${min_reads}" \

In .\modules\nf-core\fgbio\callmolecularconsensusreads\main.nf line 42:

    --min-input-base-quality ${min_baseq} \
                             ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --min-input-base-quality "${min_baseq}" \

In .\modules\nf-core\fgbio\callmolecularconsensusreads\main.nf line 43:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\fgbio\callmolecularconsensusreads\main.nf line 44:

    $args;
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args";

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fgbio\collectduplexseqmetrics\main.nf:

In .\modules\nf-core\fgbio\collectduplexseqmetrics\main.nf line 44:

    -Xmx${mem_gb}g \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${mem_gb}"g \

In .\modules\nf-core\fgbio\collectduplexseqmetrics\main.nf line 49:

    --input $grouped_bam \
            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$grouped_bam" \

In .\modules\nf-core\fgbio\collectduplexseqmetrics\main.nf line 50:

    --output ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}" \

In .\modules\nf-core\fgbio\collectduplexseqmetrics\main.nf line 51:

    $intervals \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$intervals" \

In .\modules\nf-core\fgbio\collectduplexseqmetrics\main.nf line 52:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fgbio\copyumifromreadname\main.nf:

In .\modules\nf-core\fgbio\copyumifromreadname\main.nf line 37:

    -Xmx${mem_gb}g \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${mem_gb}"g \

In .\modules\nf-core\fgbio\copyumifromreadname\main.nf line 41:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\fgbio\copyumifromreadname\main.nf line 42:

    --input ${bam} \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${bam}" \

In .\modules\nf-core\fgbio\copyumifromreadname\main.nf line 43:

    --output ${prefix}.bam
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".bam

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fgbio\fastqtobam\main.nf:

In .\modules\nf-core\fgbio\fastqtobam\main.nf line 41:

    -Xmx${mem_gb}g \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${mem_gb}"g \

In .\modules\nf-core\fgbio\fastqtobam\main.nf line 45:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\fgbio\fastqtobam\main.nf line 46:

    --input ${reads} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${reads}" \

In .\modules\nf-core\fgbio\fastqtobam\main.nf line 47:

    --output ${prefix}.${suffix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${suffix}" \

In .\modules\nf-core\fgbio\fastqtobam\main.nf line 48:

    ${sample_name} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${sample_name}" \

In .\modules\nf-core\fgbio\fastqtobam\main.nf line 49:

    ${library_name}
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${library_name}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fgbio\filterconsensusreads\main.nf:

In .\modules\nf-core\fgbio\filterconsensusreads\main.nf line 42:

    -Xmx${mem_gb}g \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${mem_gb}"g \

In .\modules\nf-core\fgbio\filterconsensusreads\main.nf line 46:

    --input $bam \
            ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$bam" \

In .\modules\nf-core\fgbio\filterconsensusreads\main.nf line 47:

    --output ${prefix}.bam \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".bam \

In .\modules\nf-core\fgbio\filterconsensusreads\main.nf line 48:

    --ref ${fasta} \
          ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ref "${fasta}" \

In .\modules\nf-core\fgbio\filterconsensusreads\main.nf line 49:

    --min-reads ${min_reads} \
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --min-reads "${min_reads}" \

In .\modules\nf-core\fgbio\filterconsensusreads\main.nf line 50:

    --min-base-quality ${min_baseq} \
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --min-base-quality "${min_baseq}" \

In .\modules\nf-core\fgbio\filterconsensusreads\main.nf line 51:

    --max-base-error-rate ${max_base_error_rate} \
                          ^--------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --max-base-error-rate "${max_base_error_rate}" \

In .\modules\nf-core\fgbio\filterconsensusreads\main.nf line 52:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fgbio\groupreadsbyumi\main.nf:

In .\modules\nf-core\fgbio\groupreadsbyumi\main.nf line 40:

    -Xmx${mem_gb}g \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${mem_gb}"g \

In .\modules\nf-core\fgbio\groupreadsbyumi\main.nf line 43:

    -s $strategy \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -s "$strategy" \

In .\modules\nf-core\fgbio\groupreadsbyumi\main.nf line 44:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fgbio\groupreadsbyumi\main.nf line 45:

    -i $bam \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bam" \

In .\modules\nf-core\fgbio\groupreadsbyumi\main.nf line 46:

    -o ${prefix}.bam \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".bam \

In .\modules\nf-core\fgbio\groupreadsbyumi\main.nf line 47:

    -f ${prefix}_histogram.txt
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -f "${prefix}"_histogram.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fgbio\sortbam\main.nf:

In .\modules\nf-core\fgbio\sortbam\main.nf line 37:

fgbio -Xmx${mem_gb}g \
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
fgbio -Xmx"${mem_gb}"g \

In .\modules\nf-core\fgbio\sortbam\main.nf line 41:

    -i $bam \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bam" \

In .\modules\nf-core\fgbio\sortbam\main.nf line 42:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fgbio\sortbam\main.nf line 43:

    -o ${prefix}.bam
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".bam

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fgbio\zipperbams\main.nf:

In .\modules\nf-core\fgbio\zipperbams\main.nf line 43:

fgbio -Xmx${mem_gb}g \
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
fgbio -Xmx"${mem_gb}"g \

In .\modules\nf-core\fgbio\zipperbams\main.nf line 44:

    --compression ${compression} \
                  ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --compression "${compression}" \

In .\modules\nf-core\fgbio\zipperbams\main.nf line 47:

    --unmapped ${unmapped_bam} \
               ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --unmapped "${unmapped_bam}" \

In .\modules\nf-core\fgbio\zipperbams\main.nf line 48:

    --input ${mapped_bam} \
            ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${mapped_bam}" \

In .\modules\nf-core\fgbio\zipperbams\main.nf line 49:

    --ref ${fasta} \
          ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ref "${fasta}" \

In .\modules\nf-core\fgbio\zipperbams\main.nf line 50:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\fgbio\zipperbams\main.nf line 51:

    --output ${prefix}.bam
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".bam

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\filtlong\main.nf:

In .\modules\nf-core\filtlong\main.nf line 28:

    $short_reads \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$short_reads" \

In .\modules\nf-core\filtlong\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\filtlong\main.nf line 30:

    $longreads \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$longreads" \

In .\modules\nf-core\filtlong\main.nf line 31:

    2> >(tee ${prefix}.log >&2) \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    2> >(tee "${prefix}".log >&2) \

In .\modules\nf-core\filtlong\main.nf line 32:

    | gzip -n > ${prefix}.fastq.gz
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | gzip -n > "${prefix}".fastq.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\find\concatenate\main.nf:

In .\modules\nf-core\find\concatenate\main.nf line 53:

find . -maxdepth 1 \( -not -name '.*'  ${pattern_string} \) \
                                       ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
find . -maxdepth 1 \( -not -name '.*'  "${pattern_string}" \) \

In .\modules\nf-core\find\concatenate\main.nf line 54:

     -exec sh -c "${command1} ${args} {} ${command2} >> ${prefix}" \;
                 ^-- SC2156 (warning): Injecting filenames is fragile and insecure. Use parameters.

For more information:
  https://www.shellcheck.net/wiki/SC2156 -- Injecting filenames is fragile an...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\find\unpigz\main.nf:

In .\modules\nf-core\find\unpigz\main.nf line 29:

while IFS= read -r -d \$'\0' file; do
^-- SC1073 (error): Couldn't parse this while loop. Fix to allow more checks.
                                   ^-- SC1061 (error): Couldn't find 'done' for this 'do'.

In .\modules\nf-core\find\unpigz\main.nf line 35:

        > ungzipped/\$( basename \$file .gz )
                      ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
                      ^-- SC1062 (error): Expected 'done' matching previously mentioned 'do'.
                      ^-- SC1072 (error): Expected 'done'. Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1061 -- Couldn't find 'done' for this 'do'.
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1062 -- Expected 'done' matching previous...

ShellCheck results for .\modules\nf-core\flash\main.nf:

In .\modules\nf-core\flash\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\flash\main.nf line 32:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\flash\main.nf line 34:

    ${reads[0]} \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reads[0]}" \

In .\modules\nf-core\flash\main.nf line 35:

    ${reads[1]}
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reads[1]}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\flye\main.nf:

In .\modules\nf-core\flye\main.nf line 33:

    $mode \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$mode" \

In .\modules\nf-core\flye\main.nf line 34:

    $reads \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads" \

In .\modules\nf-core\flye\main.nf line 37:

    $task.cpus \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$task".cpus \

In .\modules\nf-core\flye\main.nf line 38:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

In .\modules\nf-core\flye\main.nf line 40:

gzip -c assembly.fasta > ${prefix}.assembly.fasta.gz
                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip -c assembly.fasta > "${prefix}".assembly.fasta.gz

In .\modules\nf-core\flye\main.nf line 41:

gzip -c assembly_graph.gfa > ${prefix}.assembly_graph.gfa.gz
                             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip -c assembly_graph.gfa > "${prefix}".assembly_graph.gfa.gz

In .\modules\nf-core\flye\main.nf line 42:

gzip -c assembly_graph.gv > ${prefix}.assembly_graph.gv.gz
                            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip -c assembly_graph.gv > "${prefix}".assembly_graph.gv.gz

In .\modules\nf-core\flye\main.nf line 43:

mv assembly_info.txt ${prefix}.assembly_info.txt
                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv assembly_info.txt "${prefix}".assembly_info.txt

In .\modules\nf-core\flye\main.nf line 44:

mv flye.log ${prefix}.flye.log
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv flye.log "${prefix}".flye.log

In .\modules\nf-core\flye\main.nf line 45:

mv params.json ${prefix}.params.json
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv params.json "${prefix}".params.json

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\foldcomp\compress\main.nf:

In .\modules\nf-core\foldcomp\compress\main.nf line 27:

    -t ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "${task.cpus}" \

In .\modules\nf-core\foldcomp\compress\main.nf line 28:

    ${pdb} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${pdb}" \

In .\modules\nf-core\foldcomp\compress\main.nf line 29:

    ${prefix}${ext} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
             ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}""${ext}" \

In .\modules\nf-core\foldcomp\compress\main.nf line 30:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\foldcomp\decompress\main.nf:

In .\modules\nf-core\foldcomp\decompress\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\foldcomp\decompress\main.nf line 27:

    -t ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "${task.cpus}" \

In .\modules\nf-core\foldcomp\decompress\main.nf line 28:

    ${fcz}
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fcz}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\foldmason\createdb\main.nf:

In .\modules\nf-core\foldmason\createdb\main.nf line 25:

    ${structures} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${structures}" \

In .\modules\nf-core\foldmason\createdb\main.nf line 26:

    ${prefix} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}" \

In .\modules\nf-core\foldmason\createdb\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\foldmason\createdb\main.nf line 28:

    --threads $task.cpus
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\foldmason\easymsa\main.nf:

In .\modules\nf-core\foldmason\easymsa\main.nf line 30:

    ${pdbs} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${pdbs}" \

In .\modules\nf-core\foldmason\easymsa\main.nf line 31:

    ${prefix} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}" \

In .\modules\nf-core\foldmason\easymsa\main.nf line 33:

    ${options_tree} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${options_tree}" \

In .\modules\nf-core\foldmason\easymsa\main.nf line 34:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\foldmason\easymsa\main.nf line 35:

    --threads $task.cpus
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus

In .\modules\nf-core\foldmason\easymsa\main.nf line 38:

    pigz -p ${task.cpus} ${prefix}_3di.fa
            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    pigz -p "${task.cpus}" "${prefix}"_3di.fa

In .\modules\nf-core\foldmason\easymsa\main.nf line 39:

    pigz -p ${task.cpus} ${prefix}_aa.fa
            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    pigz -p "${task.cpus}" "${prefix}"_aa.fa

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\foldmason\msa2lddtreport\main.nf:

In .\modules\nf-core\foldmason\msa2lddtreport\main.nf line 28:

    ${meta.id} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${meta.id}" \

In .\modules\nf-core\foldmason\msa2lddtreport\main.nf line 29:

    ${msa} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${msa}" \

In .\modules\nf-core\foldmason\msa2lddtreport\main.nf line 30:

    ${prefix}.html \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".html \

In .\modules\nf-core\foldmason\msa2lddtreport\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\foldmason\msa2lddtreport\main.nf line 32:

    ${options_tree} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${options_tree}" \

In .\modules\nf-core\foldmason\msa2lddtreport\main.nf line 33:

    --threads $task.cpus
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\foldseek\createdb\main.nf:

In .\modules\nf-core\foldseek\createdb\main.nf line 24:

mkdir -p ${prefix}
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mkdir -p "${prefix}"

In .\modules\nf-core\foldseek\createdb\main.nf line 27:

    ${pdb} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${pdb}" \

In .\modules\nf-core\foldseek\createdb\main.nf line 28:

    ${prefix}/${prefix} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"/"${prefix}" \

In .\modules\nf-core\foldseek\createdb\main.nf line 29:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\foldseek\easysearch\main.nf:

In .\modules\nf-core\foldseek\easysearch\main.nf line 27:

    ${pdb} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${pdb}" \

In .\modules\nf-core\foldseek\easysearch\main.nf line 28:

    ${db}/${meta_db.id} \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
          ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${db}"/"${meta_db.id}" \

In .\modules\nf-core\foldseek\easysearch\main.nf line 29:

    ${prefix}.m8 \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".m8 \

In .\modules\nf-core\foldseek\easysearch\main.nf line 31:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fq\generate\main.nf:

In .\modules\nf-core\fq\generate\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fq\generate\main.nf line 26:

    ${prefix}_R1.fastq.gz ${prefix}_R2.fastq.gz
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"_R1.fastq.gz "${prefix}"_R2.fastq.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fq\lint\main.nf:

In .\modules\nf-core\fq\lint\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fq\lint\main.nf line 26:

    $fastq > ${prefix}.fq_lint.txt
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fastq" > "${prefix}".fq_lint.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fq\subsample\main.nf:

In .\modules\nf-core\fq\subsample\main.nf line 45:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\fq\subsample\main.nf line 46:

    $fastq \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fastq" \

In .\modules\nf-core\fq\subsample\main.nf line 47:

    $fastq1_output \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fastq1_output" \

In .\modules\nf-core\fq\subsample\main.nf line 48:

    $fastq2_output
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fastq2_output"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fqtk\main.nf:

In .\modules\nf-core\fqtk\main.nf line 38:

        --inputs ${fastqs} \
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        --inputs "${fastqs}" \

In .\modules\nf-core\fqtk\main.nf line 39:

        --read-structures ${read_structures} \
                          ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        --read-structures "${read_structures}" \

In .\modules\nf-core\fqtk\main.nf line 41:

        --sample-metadata ${sample_sheet} \
                          ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        --sample-metadata "${sample_sheet}" \

In .\modules\nf-core\fqtk\main.nf line 42:

        ${args}
        ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\freebayes\main.nf:

In .\modules\nf-core\freebayes\main.nf line 36:

    -f $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -f "$fasta" \

In .\modules\nf-core\freebayes\main.nf line 37:

    $targets_file \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$targets_file" \

In .\modules\nf-core\freebayes\main.nf line 38:

    $samples_file \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$samples_file" \

In .\modules\nf-core\freebayes\main.nf line 39:

    $populations_file \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$populations_file" \

In .\modules\nf-core\freebayes\main.nf line 40:

    $cnv_file \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$cnv_file" \

In .\modules\nf-core\freebayes\main.nf line 41:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\freebayes\main.nf line 42:

    $input > ${prefix}.vcf
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" > "${prefix}".vcf

In .\modules\nf-core\freebayes\main.nf line 44:

bgzip ${prefix}.vcf
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bgzip "${prefix}".vcf

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\freyja\boot\main.nf:

In .\modules\nf-core\freyja\boot\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\freyja\boot\main.nf line 32:

    --nt $task.cpus \
         ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nt "$task".cpus \

In .\modules\nf-core\freyja\boot\main.nf line 33:

    --nb $repeats \
         ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --nb "$repeats" \

In .\modules\nf-core\freyja\boot\main.nf line 34:

    --output_base $prefix \
                  ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output_base "$prefix" \

In .\modules\nf-core\freyja\boot\main.nf line 35:

    --barcodes $barcodes \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --barcodes "$barcodes" \

In .\modules\nf-core\freyja\boot\main.nf line 36:

    --meta $lineages_meta \
           ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --meta "$lineages_meta" \

In .\modules\nf-core\freyja\boot\main.nf line 37:

    $variants \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$variants" \

In .\modules\nf-core\freyja\boot\main.nf line 38:

    $depths
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$depths"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\freyja\demix\main.nf:

In .\modules\nf-core\freyja\demix\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\freyja\demix\main.nf line 30:

    --output ${prefix}.tsv \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".tsv \

In .\modules\nf-core\freyja\demix\main.nf line 31:

    --barcodes $barcodes \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --barcodes "$barcodes" \

In .\modules\nf-core\freyja\demix\main.nf line 32:

    --meta $lineages_meta \
           ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --meta "$lineages_meta" \

In .\modules\nf-core\freyja\demix\main.nf line 33:

    $variants \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$variants" \

In .\modules\nf-core\freyja\demix\main.nf line 34:

    $depths
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$depths"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\freyja\update\main.nf:

In .\modules\nf-core\freyja\update\main.nf line 26:

mkdir -p $db_name
         ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mkdir -p "$db_name"

In .\modules\nf-core\freyja\update\main.nf line 29:

    --outdir $db_name
             ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outdir "$db_name"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\freyja\variants\main.nf:

In .\modules\nf-core\freyja\variants\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\freyja\variants\main.nf line 29:

    --ref $fasta \
          ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ref "$fasta" \

In .\modules\nf-core\freyja\variants\main.nf line 30:

    --variants ${prefix}.variants.tsv \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variants "${prefix}".variants.tsv \

In .\modules\nf-core\freyja\variants\main.nf line 31:

    --depths ${prefix}.depth.tsv \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --depths "${prefix}".depth.tsv \

In .\modules\nf-core\freyja\variants\main.nf line 32:

    $bam
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fusioncatcher\build\main.nf:

In .\modules\nf-core\fusioncatcher\build\main.nf line 25:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\fusioncatcher\build\main.nf line 26:

    --output=${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output="${prefix}" \

In .\modules\nf-core\fusioncatcher\build\main.nf line 27:

    --threads=${task.cpus}
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads="${task.cpus}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\fusioncatcher\fusioncatcher\main.nf:

In .\modules\nf-core\fusioncatcher\fusioncatcher\main.nf line 36:

    --input=${input} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input="${input}" \

In .\modules\nf-core\fusioncatcher\fusioncatcher\main.nf line 38:

    --data=${reference} \
           ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --data="${reference}" \

In .\modules\nf-core\fusioncatcher\fusioncatcher\main.nf line 39:

    --threads=${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads="${task.cpus}" \

In .\modules\nf-core\fusioncatcher\fusioncatcher\main.nf line 40:

    --Xmx=${avail_mem} \
          ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --Xmx="${avail_mem}" \

In .\modules\nf-core\fusioncatcher\fusioncatcher\main.nf line 41:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

In .\modules\nf-core\fusioncatcher\fusioncatcher\main.nf line 43:

mv final-list_candidate-fusion-genes.txt ${prefix}.fusion-genes.txt
                                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv final-list_candidate-fusion-genes.txt "${prefix}".fusion-genes.txt

In .\modules\nf-core\fusioncatcher\fusioncatcher\main.nf line 44:

mv summary_candidate_fusions.txt ${prefix}.summary.txt
                                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv summary_candidate_fusions.txt "${prefix}".summary.txt

In .\modules\nf-core\fusioncatcher\fusioncatcher\main.nf line 45:

mv fusioncatcher.log ${prefix}.log
                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv fusioncatcher.log "${prefix}".log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\galah\main.nf:

In .\modules\nf-core\galah\main.nf line 34:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\galah\main.nf line 35:

    --genome-fasta-files ${bins} \
                         ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --genome-fasta-files "${bins}" \

In .\modules\nf-core\galah\main.nf line 36:

    ${qc_input} \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${qc_input}" \

In .\modules\nf-core\galah\main.nf line 37:

    --output-cluster-definition ${prefix}.tsv \
                                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-cluster-definition "${prefix}".tsv \

In .\modules\nf-core\galah\main.nf line 38:

    --output-representative-fasta-directory ${prefix} \
                                            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-representative-fasta-directory "${prefix}" \

In .\modules\nf-core\galah\main.nf line 39:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gamma\gamma\main.nf:

In .\modules\nf-core\gamma\gamma\main.nf line 31:

if [[ ${fasta} == *.gz ]]
^-- SC1046 (error): Couldn't find 'fi' for this 'if'.
^-- SC1073 (error): Couldn't parse this if expression. Fix to allow more checks.

In .\modules\nf-core\gamma\gamma\main.nf line 33:

    FNAME=\$(basename ${fasta} .gz)
            ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
            ^-- SC1047 (error): Expected 'fi' matching previously mentioned 'if'.
            ^-- SC1072 (error): Expected 'fi'. Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1046 -- Couldn't find 'fi' for this 'if'.
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1047 -- Expected 'fi' matching previously...

ShellCheck results for .\modules\nf-core\gangstr\main.nf:

In .\modules\nf-core\gangstr\main.nf line 31:

    --bam ${input} \
          ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bam "${input}" \

In .\modules\nf-core\gangstr\main.nf line 32:

    --ref ${fasta} \
          ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ref "${fasta}" \

In .\modules\nf-core\gangstr\main.nf line 33:

    --regions ${ref_regions} \
              ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --regions "${ref_regions}" \

In .\modules\nf-core\gangstr\main.nf line 34:

    --out ${prefix} \
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --out "${prefix}" \

In .\modules\nf-core\gangstr\main.nf line 35:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ganon\buildcustom\main.nf:

In .\modules\nf-core\ganon\buildcustom\main.nf line 32:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\ganon\buildcustom\main.nf line 33:

    ${input_cmd} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_cmd}" \

In .\modules\nf-core\ganon\buildcustom\main.nf line 34:

    --db-prefix ${prefix} \
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --db-prefix "${prefix}" \

In .\modules\nf-core\ganon\buildcustom\main.nf line 35:

    ${taxonomy_args} \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${taxonomy_args}" \

In .\modules\nf-core\ganon\buildcustom\main.nf line 36:

    ${genome_size_args} \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${genome_size_args}" \

In .\modules\nf-core\ganon\buildcustom\main.nf line 37:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ganon\classify\main.nf:

In .\modules\nf-core\ganon\classify\main.nf line 30:

dbprefix=\$(find -L . -name '*.*ibf' | sed 's/\.h\?ibf\$//')
^------^ SC2034 (warning): dbprefix appears unused. Verify use (or export if used externally).
           ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
           ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- dbprefix appears unused. Verify u...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\ganon\report\main.nf:

In .\modules\nf-core\ganon\report\main.nf line 25:

dbprefix=\$(find -L . -name '*.*ibf' | sed 's/\.h\?ibf\$//')
^------^ SC2034 (warning): dbprefix appears unused. Verify use (or export if used externally).
           ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
           ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- dbprefix appears unused. Verify u...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\ganon\table\main.nf:

In .\modules\nf-core\ganon\table\main.nf line 25:

    --input ${tre} \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${tre}" \

In .\modules\nf-core\ganon\table\main.nf line 26:

    --output-file ${prefix}.txt \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-file "${prefix}".txt \

In .\modules\nf-core\ganon\table\main.nf line 27:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gappa\examineassign\main.nf:

In .\modules\nf-core\gappa\examineassign\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gappa\examineassign\main.nf line 32:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\gappa\examineassign\main.nf line 33:

    --jplace-path $jplace \
                  ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --jplace-path "$jplace" \

In .\modules\nf-core\gappa\examineassign\main.nf line 34:

    --taxon-file $taxonomy \
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --taxon-file "$taxonomy" \

In .\modules\nf-core\gappa\examineassign\main.nf line 35:

    --file-prefix ${prefix}.
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --file-prefix "${prefix}".

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gappa\examinegraft\main.nf:

In .\modules\nf-core\gappa\examinegraft\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gappa\examinegraft\main.nf line 28:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\gappa\examinegraft\main.nf line 29:

    --file-prefix ${prefix}. \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --file-prefix "${prefix}". \

In .\modules\nf-core\gappa\examinegraft\main.nf line 30:

    --jplace-path $jplace
                  ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --jplace-path "$jplace"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gappa\examineheattree\main.nf:

In .\modules\nf-core\gappa\examineheattree\main.nf line 32:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\gappa\examineheattree\main.nf line 33:

    --file-prefix ${prefix}. \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --file-prefix "${prefix}". \

In .\modules\nf-core\gappa\examineheattree\main.nf line 34:

    --jplace-path $jplace \
                  ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --jplace-path "$jplace" \

In .\modules\nf-core\gappa\examineheattree\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gappa\examineheattree\main.nf line 36:

    --log-file ${prefix}.log
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --log-file "${prefix}".log

In .\modules\nf-core\gappa\examineheattree\main.nf line 38:

grep '^ *At' ${prefix}.log > ${prefix}.colours.txt
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
grep '^ *At' "${prefix}".log > "${prefix}".colours.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk\indelrealigner\main.nf:

In .\modules\nf-core\gatk\indelrealigner\main.nf line 40:

    -Xmx${avail_mem}M \
        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${avail_mem}"M \

In .\modules\nf-core\gatk\indelrealigner\main.nf line 42:

    -R ${fasta} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -R "${fasta}" \

In .\modules\nf-core\gatk\indelrealigner\main.nf line 43:

    -I ${bam} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -I "${bam}" \

In .\modules\nf-core\gatk\indelrealigner\main.nf line 44:

    --targetIntervals ${intervals} \
                      ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --targetIntervals "${intervals}" \

In .\modules\nf-core\gatk\indelrealigner\main.nf line 45:

    ${known} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${known}" \

In .\modules\nf-core\gatk\indelrealigner\main.nf line 46:

    -o ${prefix}.bam \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".bam \

In .\modules\nf-core\gatk\indelrealigner\main.nf line 47:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk\realignertargetcreator\main.nf:

In .\modules\nf-core\gatk\realignertargetcreator\main.nf line 39:

    -Xmx${avail_mem}M \
        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${avail_mem}"M \

In .\modules\nf-core\gatk\realignertargetcreator\main.nf line 41:

    -nt ${task.cpus} \
        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -nt "${task.cpus}" \

In .\modules\nf-core\gatk\realignertargetcreator\main.nf line 42:

    -I ${bam} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -I "${bam}" \

In .\modules\nf-core\gatk\realignertargetcreator\main.nf line 43:

    -R ${fasta} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -R "${fasta}" \

In .\modules\nf-core\gatk\realignertargetcreator\main.nf line 44:

    -o ${prefix}.intervals \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".intervals \

In .\modules\nf-core\gatk\realignertargetcreator\main.nf line 45:

    ${known} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${known}" \

In .\modules\nf-core\gatk\realignertargetcreator\main.nf line 46:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk\unifiedgenotyper\main.nf:

In .\modules\nf-core\gatk\unifiedgenotyper\main.nf line 45:

    -Xmx${avail_mem}M \
        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${avail_mem}"M \

In .\modules\nf-core\gatk\unifiedgenotyper\main.nf line 46:

    -nt ${task.cpus} \
        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -nt "${task.cpus}" \

In .\modules\nf-core\gatk\unifiedgenotyper\main.nf line 48:

    -I ${bam} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -I "${bam}" \

In .\modules\nf-core\gatk\unifiedgenotyper\main.nf line 49:

    -R ${fasta} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -R "${fasta}" \

In .\modules\nf-core\gatk\unifiedgenotyper\main.nf line 50:

    ${contamination_file} \
    ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${contamination_file}" \

In .\modules\nf-core\gatk\unifiedgenotyper\main.nf line 51:

    ${dbsnp_file} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${dbsnp_file}" \

In .\modules\nf-core\gatk\unifiedgenotyper\main.nf line 52:

    ${comp_file} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${comp_file}" \

In .\modules\nf-core\gatk\unifiedgenotyper\main.nf line 53:

    ${intervals_file} \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${intervals_file}" \

In .\modules\nf-core\gatk\unifiedgenotyper\main.nf line 54:

    -o ${prefix}.vcf \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".vcf \

In .\modules\nf-core\gatk\unifiedgenotyper\main.nf line 55:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

In .\modules\nf-core\gatk\unifiedgenotyper\main.nf line 57:

bgzip ${prefix}.vcf
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bgzip "${prefix}".vcf

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\addorreplacereadgroups\main.nf:

In .\modules\nf-core\gatk4\addorreplacereadgroups\main.nf line 42:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gatk4\addorreplacereadgroups\main.nf line 43:

    $reference \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference" \

In .\modules\nf-core\gatk4\addorreplacereadgroups\main.nf line 44:

    $create_index \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$create_index" \

In .\modules\nf-core\gatk4\addorreplacereadgroups\main.nf line 45:

    --INPUT ${bam} \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --INPUT "${bam}" \

In .\modules\nf-core\gatk4\addorreplacereadgroups\main.nf line 46:

    --OUTPUT ${prefix}.${suffix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --OUTPUT "${prefix}"."${suffix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\annotateintervals\main.nf:

In .\modules\nf-core\gatk4\annotateintervals\main.nf line 45:

    ${inputs} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${inputs}" \

In .\modules\nf-core\gatk4\annotateintervals\main.nf line 46:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\gatk4\annotateintervals\main.nf line 47:

    --output ${prefix}.tsv \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".tsv \

In .\modules\nf-core\gatk4\annotateintervals\main.nf line 48:

    ${mappability_track} \
    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${mappability_track}" \

In .\modules\nf-core\gatk4\annotateintervals\main.nf line 49:

    ${segmental_duplication_tracks} \
    ^-----------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${segmental_duplication_tracks}" \

In .\modules\nf-core\gatk4\annotateintervals\main.nf line 51:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\applybqsr\main.nf:

In .\modules\nf-core\gatk4\applybqsr\main.nf line 38:

    --input $input \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$input" \

In .\modules\nf-core\gatk4\applybqsr\main.nf line 39:

    --output ${prefix}.${input.getExtension()} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${input.getExtension()}" \

In .\modules\nf-core\gatk4\applybqsr\main.nf line 40:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\applybqsr\main.nf line 41:

    --bqsr-recal-file $bqsr_table \
                      ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bqsr-recal-file "$bqsr_table" \

In .\modules\nf-core\gatk4\applybqsr\main.nf line 42:

    $interval_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval_command" \

In .\modules\nf-core\gatk4\applybqsr\main.nf line 44:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\applyvqsr\main.nf:

In .\modules\nf-core\gatk4\applyvqsr\main.nf line 38:

    --variant ${vcf} \
              ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "${vcf}" \

In .\modules\nf-core\gatk4\applyvqsr\main.nf line 39:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\applyvqsr\main.nf line 40:

    $reference_command \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference_command" \

In .\modules\nf-core\gatk4\applyvqsr\main.nf line 41:

    --tranches-file $tranches \
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --tranches-file "$tranches" \

In .\modules\nf-core\gatk4\applyvqsr\main.nf line 42:

    --recal-file $recal \
                 ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --recal-file "$recal" \

In .\modules\nf-core\gatk4\applyvqsr\main.nf line 44:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\asereadcounter\main.nf:

In .\modules\nf-core\gatk4\asereadcounter\main.nf line 40:

    --output ${prefix}_ase.csv \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"_ase.csv \

In .\modules\nf-core\gatk4\asereadcounter\main.nf line 41:

    --input ${bam} \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${bam}" \

In .\modules\nf-core\gatk4\asereadcounter\main.nf line 42:

    --variant ${vcf} \
              ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "${vcf}" \

In .\modules\nf-core\gatk4\asereadcounter\main.nf line 43:

    $reference_command \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference_command" \

In .\modules\nf-core\gatk4\asereadcounter\main.nf line 44:

    $intervals_command \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$intervals_command" \

In .\modules\nf-core\gatk4\asereadcounter\main.nf line 45:

    $dictionary_command \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$dictionary_command" \

In .\modules\nf-core\gatk4\asereadcounter\main.nf line 47:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\baserecalibrator\main.nf:

In .\modules\nf-core\gatk4\baserecalibrator\main.nf line 40:

    --input $input \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$input" \

In .\modules\nf-core\gatk4\baserecalibrator\main.nf line 41:

    --output ${prefix}.table \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".table \

In .\modules\nf-core\gatk4\baserecalibrator\main.nf line 42:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\baserecalibrator\main.nf line 43:

    $interval_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval_command" \

In .\modules\nf-core\gatk4\baserecalibrator\main.nf line 44:

    $sites_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sites_command" \

In .\modules\nf-core\gatk4\baserecalibrator\main.nf line 46:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\bedtointervallist\main.nf:

In .\modules\nf-core\gatk4\bedtointervallist\main.nf line 34:

    --INPUT $bed \
            ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --INPUT "$bed" \

In .\modules\nf-core\gatk4\bedtointervallist\main.nf line 35:

    --OUTPUT ${prefix}.interval_list \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --OUTPUT "${prefix}".interval_list \

In .\modules\nf-core\gatk4\bedtointervallist\main.nf line 36:

    --SEQUENCE_DICTIONARY $dict \
                          ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --SEQUENCE_DICTIONARY "$dict" \

In .\modules\nf-core\gatk4\bedtointervallist\main.nf line 38:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\calculatecontamination\main.nf:

In .\modules\nf-core\gatk4\calculatecontamination\main.nf line 35:

    --input $pileup \
            ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$pileup" \

In .\modules\nf-core\gatk4\calculatecontamination\main.nf line 36:

    --output ${prefix}.contamination.table \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".contamination.table \

In .\modules\nf-core\gatk4\calculatecontamination\main.nf line 37:

    $matched_command \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$matched_command" \

In .\modules\nf-core\gatk4\calculatecontamination\main.nf line 39:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\calibratedragstrmodel\main.nf:

In .\modules\nf-core\gatk4\calibratedragstrmodel\main.nf line 37:

    --input ${bam} \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${bam}" \

In .\modules\nf-core\gatk4\calibratedragstrmodel\main.nf line 38:

    --output ${prefix}.txt \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".txt \

In .\modules\nf-core\gatk4\calibratedragstrmodel\main.nf line 39:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\gatk4\calibratedragstrmodel\main.nf line 40:

    --str-table-path ${strtablefile} \
                     ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --str-table-path "${strtablefile}" \

In .\modules\nf-core\gatk4\calibratedragstrmodel\main.nf line 41:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\gatk4\calibratedragstrmodel\main.nf line 43:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\cnnscorevariants\main.nf:

In .\modules\nf-core\gatk4\cnnscorevariants\main.nf line 47:

    --variant $vcf \
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "$vcf" \

In .\modules\nf-core\gatk4\cnnscorevariants\main.nf line 48:

    --output ${prefix}.cnn.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".cnn.vcf.gz \

In .\modules\nf-core\gatk4\cnnscorevariants\main.nf line 49:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\cnnscorevariants\main.nf line 50:

    $interval_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval_command" \

In .\modules\nf-core\gatk4\cnnscorevariants\main.nf line 51:

    $aligned_input_cmd \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$aligned_input_cmd" \

In .\modules\nf-core\gatk4\cnnscorevariants\main.nf line 52:

    $architecture_cmd \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$architecture_cmd" \

In .\modules\nf-core\gatk4\cnnscorevariants\main.nf line 53:

    $weights_cmd \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$weights_cmd" \

In .\modules\nf-core\gatk4\cnnscorevariants\main.nf line 55:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\collectreadcounts\main.nf:

In .\modules\nf-core\gatk4\collectreadcounts\main.nf line 42:

    --input $input \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$input" \

In .\modules\nf-core\gatk4\collectreadcounts\main.nf line 43:

    --intervals $intervals \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --intervals "$intervals" \

In .\modules\nf-core\gatk4\collectreadcounts\main.nf line 44:

    --output ${prefix}.$extension \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."$extension" \

In .\modules\nf-core\gatk4\collectreadcounts\main.nf line 45:

    $reference \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference" \

In .\modules\nf-core\gatk4\collectreadcounts\main.nf line 47:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\collectsvevidence\main.nf:

In .\modules\nf-core\gatk4\collectsvevidence\main.nf line 44:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\gatk4\collectsvevidence\main.nf line 45:

    --input ${input} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${input}" \

In .\modules\nf-core\gatk4\collectsvevidence\main.nf line 46:

    --sr-file ${prefix}.sr.txt.gz \
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --sr-file "${prefix}".sr.txt.gz \

In .\modules\nf-core\gatk4\collectsvevidence\main.nf line 47:

    --pe-file ${prefix}.pe.txt.gz \
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --pe-file "${prefix}".pe.txt.gz \

In .\modules\nf-core\gatk4\collectsvevidence\main.nf line 48:

    ${sd_vcf} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${sd_vcf}" \

In .\modules\nf-core\gatk4\collectsvevidence\main.nf line 49:

    ${reference} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reference}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\combinegvcfs\main.nf:

In .\modules\nf-core\gatk4\combinegvcfs\main.nf line 37:

    $input_list \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_list" \

In .\modules\nf-core\gatk4\combinegvcfs\main.nf line 38:

    --output ${prefix}.combined.g.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".combined.g.vcf.gz \

In .\modules\nf-core\gatk4\combinegvcfs\main.nf line 39:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\gatk4\combinegvcfs\main.nf line 41:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\composestrtablefile\main.nf:

In .\modules\nf-core\gatk4\composestrtablefile\main.nf line 34:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\composestrtablefile\main.nf line 35:

    --output ${fasta.baseName}.zip \
             ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${fasta.baseName}".zip \

In .\modules\nf-core\gatk4\composestrtablefile\main.nf line 37:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\condensedepthevidence\main.nf:

In .\modules\nf-core\gatk4\condensedepthevidence\main.nf line 42:

    --depth-evidence ${depth_evidence} \
                     ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --depth-evidence "${depth_evidence}" \

In .\modules\nf-core\gatk4\condensedepthevidence\main.nf line 43:

    --output ${prefix}.rd.txt.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".rd.txt.gz \

In .\modules\nf-core\gatk4\condensedepthevidence\main.nf line 44:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\gatk4\condensedepthevidence\main.nf line 46:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\createreadcountpanelofnormals\main.nf:

In .\modules\nf-core\gatk4\createreadcountpanelofnormals\main.nf line 34:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\gatk4\createreadcountpanelofnormals\main.nf line 35:

    ${input_list} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_list}" \

In .\modules\nf-core\gatk4\createreadcountpanelofnormals\main.nf line 36:

    --output ${prefix}.hdf5
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".hdf5

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\createsequencedictionary\main.nf:

In .\modules\nf-core\gatk4\createsequencedictionary\main.nf line 32:

    --REFERENCE $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --REFERENCE "$fasta" \

In .\modules\nf-core\gatk4\createsequencedictionary\main.nf line 33:

    --URI $fasta \
          ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --URI "$fasta" \

In .\modules\nf-core\gatk4\createsequencedictionary\main.nf line 35:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\createsomaticpanelofnormals\main.nf:

In .\modules\nf-core\gatk4\createsomaticpanelofnormals\main.nf line 37:

    --variant gendb://$genomicsdb \
                      ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant gendb://"$genomicsdb" \

In .\modules\nf-core\gatk4\createsomaticpanelofnormals\main.nf line 38:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\createsomaticpanelofnormals\main.nf line 39:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\createsomaticpanelofnormals\main.nf line 41:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\denoisereadcounts\main.nf:

In .\modules\nf-core\gatk4\denoisereadcounts\main.nf line 35:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\gatk4\denoisereadcounts\main.nf line 37:

    --input ${counts} \
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${counts}" \

In .\modules\nf-core\gatk4\denoisereadcounts\main.nf line 38:

    --count-panel-of-normals ${pon} \
                             ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --count-panel-of-normals "${pon}" \

In .\modules\nf-core\gatk4\denoisereadcounts\main.nf line 39:

    --standardized-copy-ratios ${prefix}_standardizedCR.tsv \
                               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --standardized-copy-ratios "${prefix}"_standardizedCR.tsv \

In .\modules\nf-core\gatk4\denoisereadcounts\main.nf line 40:

    --denoised-copy-ratios ${prefix}_denoisedCR.tsv
                           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --denoised-copy-ratios "${prefix}"_denoisedCR.tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\determinegermlinecontigploidy\main.nf:

In .\modules\nf-core\gatk4\determinegermlinecontigploidy\main.nf line 47:

    ${input_list} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_list}" \

In .\modules\nf-core\gatk4\determinegermlinecontigploidy\main.nf line 49:

    --output-prefix ${prefix} \
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-prefix "${prefix}" \

In .\modules\nf-core\gatk4\determinegermlinecontigploidy\main.nf line 50:

    ${intervals} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${intervals}" \

In .\modules\nf-core\gatk4\determinegermlinecontigploidy\main.nf line 51:

    ${exclude} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${exclude}" \

In .\modules\nf-core\gatk4\determinegermlinecontigploidy\main.nf line 52:

    ${contig_ploidy} \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${contig_ploidy}" \

In .\modules\nf-core\gatk4\determinegermlinecontigploidy\main.nf line 53:

    ${model} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${model}" \

In .\modules\nf-core\gatk4\determinegermlinecontigploidy\main.nf line 55:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\estimatelibrarycomplexity\main.nf:

In .\modules\nf-core\gatk4\estimatelibrarycomplexity\main.nf line 38:

    $input_list \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_list" \

In .\modules\nf-core\gatk4\estimatelibrarycomplexity\main.nf line 39:

    --OUTPUT ${prefix}.metrics \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --OUTPUT "${prefix}".metrics \

In .\modules\nf-core\gatk4\estimatelibrarycomplexity\main.nf line 40:

    $reference \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference" \

In .\modules\nf-core\gatk4\estimatelibrarycomplexity\main.nf line 42:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\fastqtosam\main.nf:

In .\modules\nf-core\gatk4\fastqtosam\main.nf line 34:

    $reads_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads_command" \

In .\modules\nf-core\gatk4\fastqtosam\main.nf line 35:

    --OUTPUT ${prefix}.bam \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --OUTPUT "${prefix}".bam \

In .\modules\nf-core\gatk4\fastqtosam\main.nf line 36:

    --SAMPLE_NAME $prefix \
                  ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --SAMPLE_NAME "$prefix" \

In .\modules\nf-core\gatk4\fastqtosam\main.nf line 38:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\filterintervals\main.nf:

In .\modules\nf-core\gatk4\filterintervals\main.nf line 37:

    $annotated_command \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$annotated_command" \

In .\modules\nf-core\gatk4\filterintervals\main.nf line 38:

    $read_counts_command \
    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$read_counts_command" \

In .\modules\nf-core\gatk4\filterintervals\main.nf line 39:

    --intervals $intervals \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --intervals "$intervals" \

In .\modules\nf-core\gatk4\filterintervals\main.nf line 40:

    --output ${prefix}.interval_list \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".interval_list \

In .\modules\nf-core\gatk4\filterintervals\main.nf line 41:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\filtermutectcalls\main.nf:

In .\modules\nf-core\gatk4\filtermutectcalls\main.nf line 43:

    --variant $vcf \
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "$vcf" \

In .\modules\nf-core\gatk4\filtermutectcalls\main.nf line 44:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\filtermutectcalls\main.nf line 45:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\filtermutectcalls\main.nf line 46:

    $orientationbias_command \
    ^----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$orientationbias_command" \

In .\modules\nf-core\gatk4\filtermutectcalls\main.nf line 47:

    $segmentation_command \
    ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$segmentation_command" \

In .\modules\nf-core\gatk4\filtermutectcalls\main.nf line 48:

    $estimate_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$estimate_command" \

In .\modules\nf-core\gatk4\filtermutectcalls\main.nf line 49:

    $table_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$table_command" \

In .\modules\nf-core\gatk4\filtermutectcalls\main.nf line 51:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\filtervarianttranches\main.nf:

In .\modules\nf-core\gatk4\filtervarianttranches\main.nf line 41:

    --variant $vcf \
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "$vcf" \

In .\modules\nf-core\gatk4\filtervarianttranches\main.nf line 42:

    $resource_list \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$resource_list" \

In .\modules\nf-core\gatk4\filtervarianttranches\main.nf line 43:

    --output ${prefix}.filtered.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".filtered.vcf.gz \

In .\modules\nf-core\gatk4\filtervarianttranches\main.nf line 45:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\gatherbqsrreports\main.nf:

In .\modules\nf-core\gatk4\gatherbqsrreports\main.nf line 34:

    $input_list \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_list" \

In .\modules\nf-core\gatk4\gatherbqsrreports\main.nf line 35:

    --output ${prefix}.table \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".table \

In .\modules\nf-core\gatk4\gatherbqsrreports\main.nf line 37:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\gatherpileupsummaries\main.nf:

In .\modules\nf-core\gatk4\gatherpileupsummaries\main.nf line 36:

    $input_list \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_list" \

In .\modules\nf-core\gatk4\gatherpileupsummaries\main.nf line 37:

    --O ${prefix}.pileups.table \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --O "${prefix}".pileups.table \

In .\modules\nf-core\gatk4\gatherpileupsummaries\main.nf line 38:

    --sequence-dictionary $dict \
                          ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --sequence-dictionary "$dict" \

In .\modules\nf-core\gatk4\gatherpileupsummaries\main.nf line 40:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\genomicsdbimport\main.nf:

In .\modules\nf-core\gatk4\genomicsdbimport\main.nf line 58:

    $input_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_command" \

In .\modules\nf-core\gatk4\genomicsdbimport\main.nf line 59:

    $genomicsdb_command \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$genomicsdb_command" \

In .\modules\nf-core\gatk4\genomicsdbimport\main.nf line 60:

    $interval_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval_command" \

In .\modules\nf-core\gatk4\genomicsdbimport\main.nf line 62:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\genotypegvcfs\main.nf:

In .\modules\nf-core\gatk4\genotypegvcfs\main.nf line 42:

    --variant $input_command \
              ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "$input_command" \

In .\modules\nf-core\gatk4\genotypegvcfs\main.nf line 43:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\genotypegvcfs\main.nf line 44:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\genotypegvcfs\main.nf line 45:

    $interval_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval_command" \

In .\modules\nf-core\gatk4\genotypegvcfs\main.nf line 46:

    $dbsnp_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$dbsnp_command" \

In .\modules\nf-core\gatk4\genotypegvcfs\main.nf line 48:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\germlinecnvcaller\main.nf:

In .\modules\nf-core\gatk4\germlinecnvcaller\main.nf line 45:

    $input_list \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_list" \

In .\modules\nf-core\gatk4\germlinecnvcaller\main.nf line 46:

    $ploidy_command \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ploidy_command" \

In .\modules\nf-core\gatk4\germlinecnvcaller\main.nf line 47:

    $output_command \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$output_command" \

In .\modules\nf-core\gatk4\germlinecnvcaller\main.nf line 48:

    --output-prefix $prefix \
                    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-prefix "$prefix" \

In .\modules\nf-core\gatk4\germlinecnvcaller\main.nf line 49:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gatk4\germlinecnvcaller\main.nf line 50:

    $intervals_command \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$intervals_command" \

In .\modules\nf-core\gatk4\germlinecnvcaller\main.nf line 51:

    $model_command
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$model_command"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\getpileupsummaries\main.nf:

In .\modules\nf-core\gatk4\getpileupsummaries\main.nf line 40:

    --input $input \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$input" \

In .\modules\nf-core\gatk4\getpileupsummaries\main.nf line 41:

    --variant $variants \
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "$variants" \

In .\modules\nf-core\gatk4\getpileupsummaries\main.nf line 42:

    --output ${prefix}.pileups.table \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".pileups.table \

In .\modules\nf-core\gatk4\getpileupsummaries\main.nf line 43:

    $reference_command \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference_command" \

In .\modules\nf-core\gatk4\getpileupsummaries\main.nf line 44:

    $interval_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval_command" \

In .\modules\nf-core\gatk4\getpileupsummaries\main.nf line 46:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\haplotypecaller\main.nf:

In .\modules\nf-core\gatk4\haplotypecaller\main.nf line 44:

    --input $input \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$input" \

In .\modules\nf-core\gatk4\haplotypecaller\main.nf line 45:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\haplotypecaller\main.nf line 46:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\haplotypecaller\main.nf line 47:

    --native-pair-hmm-threads ${task.cpus} \
                              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --native-pair-hmm-threads "${task.cpus}" \

In .\modules\nf-core\gatk4\haplotypecaller\main.nf line 48:

    $dbsnp_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$dbsnp_command" \

In .\modules\nf-core\gatk4\haplotypecaller\main.nf line 49:

    $interval_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval_command" \

In .\modules\nf-core\gatk4\haplotypecaller\main.nf line 50:

    $dragstr_command \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$dragstr_command" \

In .\modules\nf-core\gatk4\haplotypecaller\main.nf line 51:

    $bamout_command \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bamout_command" \

In .\modules\nf-core\gatk4\haplotypecaller\main.nf line 53:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\indexfeaturefile\main.nf:

In .\modules\nf-core\gatk4\indexfeaturefile\main.nf line 32:

    --input $feature_file \
            ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$feature_file" \

In .\modules\nf-core\gatk4\indexfeaturefile\main.nf line 34:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\intervallisttobed\main.nf:

In .\modules\nf-core\gatk4\intervallisttobed\main.nf line 34:

    --INPUT ${intervals} \
            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --INPUT "${intervals}" \

In .\modules\nf-core\gatk4\intervallisttobed\main.nf line 35:

    --OUTPUT ${prefix}.bed \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --OUTPUT "${prefix}".bed \

In .\modules\nf-core\gatk4\intervallisttobed\main.nf line 37:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\intervallisttools\main.nf:

In .\modules\nf-core\gatk4\intervallisttools\main.nf line 32:

mkdir ${prefix}_split
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mkdir "${prefix}"_split

In .\modules\nf-core\gatk4\intervallisttools\main.nf line 36:

    --INPUT $intervals \
            ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --INPUT "$intervals" \

In .\modules\nf-core\gatk4\intervallisttools\main.nf line 37:

    --OUTPUT ${prefix}_split \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --OUTPUT "${prefix}"_split \

In .\modules\nf-core\gatk4\intervallisttools\main.nf line 39:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\learnreadorientationmodel\main.nf:

In .\modules\nf-core\gatk4\learnreadorientationmodel\main.nf line 34:

    $input_list \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_list" \

In .\modules\nf-core\gatk4\learnreadorientationmodel\main.nf line 35:

    --output ${prefix}.tar.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".tar.gz \

In .\modules\nf-core\gatk4\learnreadorientationmodel\main.nf line 37:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\leftalignandtrimvariants\main.nf:

In .\modules\nf-core\gatk4\leftalignandtrimvariants\main.nf line 38:

    $interval_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval_command" \

In .\modules\nf-core\gatk4\leftalignandtrimvariants\main.nf line 39:

    --variant $vcf \
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "$vcf" \

In .\modules\nf-core\gatk4\leftalignandtrimvariants\main.nf line 40:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\leftalignandtrimvariants\main.nf line 41:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\leftalignandtrimvariants\main.nf line 43:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\markduplicates\main.nf:

In .\modules\nf-core\gatk4\markduplicates\main.nf line 49:

    ${input_list} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_list}" \

In .\modules\nf-core\gatk4\markduplicates\main.nf line 50:

    --OUTPUT ${prefix_bam} \
             ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --OUTPUT "${prefix_bam}" \

In .\modules\nf-core\gatk4\markduplicates\main.nf line 51:

    --METRICS_FILE ${prefix}.metrics \
                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --METRICS_FILE "${prefix}".metrics \

In .\modules\nf-core\gatk4\markduplicates\main.nf line 53:

    ${reference} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reference}" \

In .\modules\nf-core\gatk4\markduplicates\main.nf line 54:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

In .\modules\nf-core\gatk4\markduplicates\main.nf line 58:

    samtools view -Ch -T ${fasta} -o ${prefix} ${prefix_bam}
                         ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                               ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    samtools view -Ch -T "${fasta}" -o "${prefix}" "${prefix_bam}"

In .\modules\nf-core\gatk4\markduplicates\main.nf line 59:

    rm ${prefix_bam}
       ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    rm "${prefix_bam}"

In .\modules\nf-core\gatk4\markduplicates\main.nf line 60:

    samtools index ${prefix}
                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    samtools index "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\mergebamalignment\main.nf:

In .\modules\nf-core\gatk4\mergebamalignment\main.nf line 35:

    --UNMAPPED_BAM $unmapped \
                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --UNMAPPED_BAM "$unmapped" \

In .\modules\nf-core\gatk4\mergebamalignment\main.nf line 36:

    --ALIGNED_BAM $aligned \
                  ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ALIGNED_BAM "$aligned" \

In .\modules\nf-core\gatk4\mergebamalignment\main.nf line 37:

    --OUTPUT ${prefix}.bam \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --OUTPUT "${prefix}".bam \

In .\modules\nf-core\gatk4\mergebamalignment\main.nf line 38:

    --REFERENCE_SEQUENCE $fasta \
                         ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --REFERENCE_SEQUENCE "$fasta" \

In .\modules\nf-core\gatk4\mergebamalignment\main.nf line 40:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\mergemutectstats\main.nf:

In .\modules\nf-core\gatk4\mergemutectstats\main.nf line 34:

    $input_list \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_list" \

In .\modules\nf-core\gatk4\mergemutectstats\main.nf line 35:

    --output ${prefix}.vcf.gz.stats \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz.stats \

In .\modules\nf-core\gatk4\mergemutectstats\main.nf line 37:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\mergevcfs\main.nf:

In .\modules\nf-core\gatk4\mergevcfs\main.nf line 37:

    $input_list \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_list" \

In .\modules\nf-core\gatk4\mergevcfs\main.nf line 38:

    --OUTPUT ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --OUTPUT "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\mergevcfs\main.nf line 39:

    $reference_command \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference_command" \

In .\modules\nf-core\gatk4\mergevcfs\main.nf line 41:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\modelsegments\main.nf:

In .\modules\nf-core\gatk4\modelsegments\main.nf line 32:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\gatk4\modelsegments\main.nf line 34:

    --denoised-copy-ratios ${counts} \
                           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --denoised-copy-ratios "${counts}" \

In .\modules\nf-core\gatk4\modelsegments\main.nf line 36:

    --output-prefix ${prefix}
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-prefix "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\mutect2\main.nf:

In .\modules\nf-core\gatk4\mutect2\main.nf line 47:

    $inputs \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$inputs" \

In .\modules\nf-core\gatk4\mutect2\main.nf line 48:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\mutect2\main.nf line 49:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\mutect2\main.nf line 50:

    $pon_command \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$pon_command" \

In .\modules\nf-core\gatk4\mutect2\main.nf line 51:

    $gr_command \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gr_command" \

In .\modules\nf-core\gatk4\mutect2\main.nf line 52:

    $interval_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval_command" \

In .\modules\nf-core\gatk4\mutect2\main.nf line 54:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\postprocessgermlinecnvcalls\main.nf:

In .\modules\nf-core\gatk4\postprocessgermlinecnvcalls\main.nf line 41:

    $calls_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$calls_command" \

In .\modules\nf-core\gatk4\postprocessgermlinecnvcalls\main.nf line 42:

    $model_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$model_command" \

In .\modules\nf-core\gatk4\postprocessgermlinecnvcalls\main.nf line 43:

    $ploidy_command \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ploidy_command" \

In .\modules\nf-core\gatk4\postprocessgermlinecnvcalls\main.nf line 44:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gatk4\postprocessgermlinecnvcalls\main.nf line 45:

    --output-genotyped-intervals ${prefix}_genotyped_intervals.vcf.gz \
                                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-genotyped-intervals "${prefix}"_genotyped_intervals.vcf.gz \

In .\modules\nf-core\gatk4\postprocessgermlinecnvcalls\main.nf line 46:

    --output-genotyped-segments ${prefix}_genotyped_segments.vcf.gz \
                                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-genotyped-segments "${prefix}"_genotyped_segments.vcf.gz \

In .\modules\nf-core\gatk4\postprocessgermlinecnvcalls\main.nf line 47:

    --output-denoised-copy-ratios ${prefix}_denoised.vcf.gz
                                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-denoised-copy-ratios "${prefix}"_denoised.vcf.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\preprocessintervals\main.nf:

In .\modules\nf-core\gatk4\preprocessintervals\main.nf line 40:

    $include_command \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$include_command" \

In .\modules\nf-core\gatk4\preprocessintervals\main.nf line 41:

    $exclude_command \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$exclude_command" \

In .\modules\nf-core\gatk4\preprocessintervals\main.nf line 42:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\preprocessintervals\main.nf line 43:

    --output ${prefix}.interval_list \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".interval_list \

In .\modules\nf-core\gatk4\preprocessintervals\main.nf line 44:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\printreads\main.nf:

In .\modules\nf-core\gatk4\printreads\main.nf line 41:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gatk4\printreads\main.nf line 42:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\printreads\main.nf line 43:

    --input $input \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$input" \

In .\modules\nf-core\gatk4\printreads\main.nf line 44:

    --read-index $index \
                 ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --read-index "$index" \

In .\modules\nf-core\gatk4\printreads\main.nf line 45:

    --output ${prefix}.${input.getExtension()}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${input.getExtension()}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\printsvevidence\main.nf:

In .\modules\nf-core\gatk4\printsvevidence\main.nf line 53:

    ${input_files} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_files}" \

In .\modules\nf-core\gatk4\printsvevidence\main.nf line 54:

    --sequence-dictionary ${dict} \
                          ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --sequence-dictionary "${dict}" \

In .\modules\nf-core\gatk4\printsvevidence\main.nf line 55:

    ${intervals} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${intervals}" \

In .\modules\nf-core\gatk4\printsvevidence\main.nf line 56:

    ${reference} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reference}" \

In .\modules\nf-core\gatk4\printsvevidence\main.nf line 57:

    --output ${prefix}.${file_type}.txt.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${file_type}".txt.gz \

In .\modules\nf-core\gatk4\printsvevidence\main.nf line 59:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\reblockgvcf\main.nf:

In .\modules\nf-core\gatk4\reblockgvcf\main.nf line 40:

    --variant $gvcf \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "$gvcf" \

In .\modules\nf-core\gatk4\reblockgvcf\main.nf line 41:

    --output ${prefix}.rb.g.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".rb.g.vcf.gz \

In .\modules\nf-core\gatk4\reblockgvcf\main.nf line 42:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\reblockgvcf\main.nf line 43:

    $dbsnp_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$dbsnp_command" \

In .\modules\nf-core\gatk4\reblockgvcf\main.nf line 44:

    $interval_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval_command" \

In .\modules\nf-core\gatk4\reblockgvcf\main.nf line 46:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\revertsam\main.nf:

In .\modules\nf-core\gatk4\revertsam\main.nf line 33:

    --INPUT $bam \
            ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --INPUT "$bam" \

In .\modules\nf-core\gatk4\revertsam\main.nf line 34:

    --OUTPUT ${prefix}.reverted.bam \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --OUTPUT "${prefix}".reverted.bam \

In .\modules\nf-core\gatk4\revertsam\main.nf line 36:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\samtofastq\main.nf:

In .\modules\nf-core\gatk4\samtofastq\main.nf line 34:

    --INPUT $bam \
            ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --INPUT "$bam" \

In .\modules\nf-core\gatk4\samtofastq\main.nf line 35:

    $output \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$output" \

In .\modules\nf-core\gatk4\samtofastq\main.nf line 37:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\selectvariants\main.nf:

In .\modules\nf-core\gatk4\selectvariants\main.nf line 35:

    --variant $vcf \
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "$vcf" \

In .\modules\nf-core\gatk4\selectvariants\main.nf line 36:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\selectvariants\main.nf line 37:

    $interval \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval" \

In .\modules\nf-core\gatk4\selectvariants\main.nf line 39:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\shiftfasta\main.nf:

In .\modules\nf-core\gatk4\shiftfasta\main.nf line 41:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\shiftfasta\main.nf line 42:

    --output ${prefix}_shift.fasta \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"_shift.fasta \

In .\modules\nf-core\gatk4\shiftfasta\main.nf line 43:

    --shift-back-output ${prefix}_shift.back_chain \
                        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --shift-back-output "${prefix}"_shift.back_chain \

In .\modules\nf-core\gatk4\shiftfasta\main.nf line 44:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gatk4\shiftfasta\main.nf line 45:

    $seq_dict \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$seq_dict" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\sitedepthtobaf\main.nf:

In .\modules\nf-core\gatk4\sitedepthtobaf\main.nf line 42:

    --baf-evidence-output ${prefix}.baf.txt.gz \
                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --baf-evidence-output "${prefix}".baf.txt.gz \

In .\modules\nf-core\gatk4\sitedepthtobaf\main.nf line 43:

    --baf-sites-vcf ${vcf} \
                    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --baf-sites-vcf "${vcf}" \

In .\modules\nf-core\gatk4\sitedepthtobaf\main.nf line 44:

    ${site_depth_input} \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${site_depth_input}" \

In .\modules\nf-core\gatk4\sitedepthtobaf\main.nf line 45:

    ${reference} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reference}" \

In .\modules\nf-core\gatk4\sitedepthtobaf\main.nf line 47:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\splitcram\main.nf:

In .\modules\nf-core\gatk4\splitcram\main.nf line 33:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\gatk4\splitcram\main.nf line 34:

    --input ${cram} \
            ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${cram}" \

In .\modules\nf-core\gatk4\splitcram\main.nf line 35:

    --output ${prefix}.%04d.cram \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".%04d.cram \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\splitintervals\main.nf:

In .\modules\nf-core\gatk4\splitintervals\main.nf line 37:

    --output ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}" \

In .\modules\nf-core\gatk4\splitintervals\main.nf line 38:

    --intervals $intervals \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --intervals "$intervals" \

In .\modules\nf-core\gatk4\splitintervals\main.nf line 39:

    $reference \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference" \

In .\modules\nf-core\gatk4\splitintervals\main.nf line 41:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\splitncigarreads\main.nf:

In .\modules\nf-core\gatk4\splitncigarreads\main.nf line 37:

    --input $bam \
            ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$bam" \

In .\modules\nf-core\gatk4\splitncigarreads\main.nf line 38:

    --output ${prefix}.bam \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".bam \

In .\modules\nf-core\gatk4\splitncigarreads\main.nf line 39:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\splitncigarreads\main.nf line 40:

    $interval_command \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$interval_command" \

In .\modules\nf-core\gatk4\splitncigarreads\main.nf line 42:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\svannotate\main.nf:

In .\modules\nf-core\gatk4\svannotate\main.nf line 40:

    --variant ${vcf} \
              ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "${vcf}" \

In .\modules\nf-core\gatk4\svannotate\main.nf line 41:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\svannotate\main.nf line 42:

    ${intervals} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${intervals}" \

In .\modules\nf-core\gatk4\svannotate\main.nf line 43:

    ${reference} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reference}" \

In .\modules\nf-core\gatk4\svannotate\main.nf line 45:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\svcluster\main.nf:

In .\modules\nf-core\gatk4\svcluster\main.nf line 40:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\svcluster\main.nf line 41:

    --ploidy-table ${ploidy_table} \
                   ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --ploidy-table "${ploidy_table}" \

In .\modules\nf-core\gatk4\svcluster\main.nf line 42:

    ${input} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input}" \

In .\modules\nf-core\gatk4\svcluster\main.nf line 43:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\gatk4\svcluster\main.nf line 45:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\unmarkduplicates\main.nf:

In .\modules\nf-core\gatk4\unmarkduplicates\main.nf line 36:

    ${input_list} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_list}" \

In .\modules\nf-core\gatk4\unmarkduplicates\main.nf line 37:

    --output ${prefix}.bam \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".bam \

In .\modules\nf-core\gatk4\unmarkduplicates\main.nf line 38:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\variantfiltration\main.nf:

In .\modules\nf-core\gatk4\variantfiltration\main.nf line 44:

if [[ $dict_name != $dict ]]; then
                    ^---^ SC2053 (warning): Quote the right-hand side of != in [[ ]] to prevent glob matching.

In .\modules\nf-core\gatk4\variantfiltration\main.nf line 45:

    ln -s $dict $dict_name
          ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    ln -s "$dict" "$dict_name"

In .\modules\nf-core\gatk4\variantfiltration\main.nf line 50:

    --variant $vcf \
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "$vcf" \

In .\modules\nf-core\gatk4\variantfiltration\main.nf line 51:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gatk4\variantfiltration\main.nf line 52:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\variantfiltration\main.nf line 54:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2053 -- Quote the right-hand side of != i...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\variantrecalibrator\main.nf:

In .\modules\nf-core\gatk4\variantrecalibrator\main.nf line 44:

    --variant $vcf \
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "$vcf" \

In .\modules\nf-core\gatk4\variantrecalibrator\main.nf line 45:

    --output ${prefix}.recal \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".recal \

In .\modules\nf-core\gatk4\variantrecalibrator\main.nf line 46:

    --tranches-file ${prefix}.tranches \
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --tranches-file "${prefix}".tranches \

In .\modules\nf-core\gatk4\variantrecalibrator\main.nf line 47:

    $reference_command \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference_command" \

In .\modules\nf-core\gatk4\variantrecalibrator\main.nf line 49:

    $labels_command \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$labels_command" \

In .\modules\nf-core\gatk4\variantrecalibrator\main.nf line 50:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4\variantstotable\main.nf:

In .\modules\nf-core\gatk4\variantstotable\main.nf line 39:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\gatk4\variantstotable\main.nf line 40:

    --variant $vcf \
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --variant "$vcf" \

In .\modules\nf-core\gatk4\variantstotable\main.nf line 41:

    --output ${prefix}.tsv \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".tsv \

In .\modules\nf-core\gatk4\variantstotable\main.nf line 42:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\gatk4\variantstotable\main.nf line 44:

    $arguments_file_arg \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$arguments_file_arg" \

In .\modules\nf-core\gatk4\variantstotable\main.nf line 45:

    $include_intervals_arg \
    ^--------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$include_intervals_arg" \

In .\modules\nf-core\gatk4\variantstotable\main.nf line 46:

    $exclude_intervals_arg
    ^--------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$exclude_intervals_arg"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4spark\applybqsr\main.nf:

In .\modules\nf-core\gatk4spark\applybqsr\main.nf line 40:

    --input ${input} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${input}" \

In .\modules\nf-core\gatk4spark\applybqsr\main.nf line 41:

    --output ${prefix}.${input.getExtension()} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${input.getExtension()}" \

In .\modules\nf-core\gatk4spark\applybqsr\main.nf line 42:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\gatk4spark\applybqsr\main.nf line 43:

    --bqsr-recal-file ${bqsr_table} \
                      ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bqsr-recal-file "${bqsr_table}" \

In .\modules\nf-core\gatk4spark\applybqsr\main.nf line 44:

    ${interval_command} \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${interval_command}" \

In .\modules\nf-core\gatk4spark\applybqsr\main.nf line 45:

    --spark-master local[${task.cpus}] \
                         ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --spark-master local["${task.cpus}"] \

In .\modules\nf-core\gatk4spark\applybqsr\main.nf line 47:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4spark\baserecalibrator\main.nf:

In .\modules\nf-core\gatk4spark\baserecalibrator\main.nf line 41:

    --input ${input} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${input}" \

In .\modules\nf-core\gatk4spark\baserecalibrator\main.nf line 42:

    --output ${prefix}.table \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".table \

In .\modules\nf-core\gatk4spark\baserecalibrator\main.nf line 43:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\gatk4spark\baserecalibrator\main.nf line 44:

    ${interval_command} \
    ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${interval_command}" \

In .\modules\nf-core\gatk4spark\baserecalibrator\main.nf line 45:

    ${sites_command} \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${sites_command}" \

In .\modules\nf-core\gatk4spark\baserecalibrator\main.nf line 46:

    --spark-master local[${task.cpus}] \
                         ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --spark-master local["${task.cpus}"] \

In .\modules\nf-core\gatk4spark\baserecalibrator\main.nf line 48:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gatk4spark\markduplicates\main.nf:

In .\modules\nf-core\gatk4spark\markduplicates\main.nf line 40:

    ${input_list} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_list}" \

In .\modules\nf-core\gatk4spark\markduplicates\main.nf line 41:

    --output ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}" \

In .\modules\nf-core\gatk4spark\markduplicates\main.nf line 42:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\gatk4spark\markduplicates\main.nf line 43:

    --spark-master local[${task.cpus}] \
                         ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --spark-master local["${task.cpus}"] \

In .\modules\nf-core\gatk4spark\markduplicates\main.nf line 45:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gawk\main.nf:

In .\modules\nf-core\gawk\main.nf line 44:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\gawk\main.nf line 45:

    ${program} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${program}" \

In .\modules\nf-core\gawk\main.nf line 46:

    ${input_cmd} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_cmd}" \

In .\modules\nf-core\gawk\main.nf line 47:

    ${output}
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${output}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gecco\run\main.nf:

In .\modules\nf-core\gecco\run\main.nf line 41:

for i in \$(find -name '${input.baseName}*' -type f); do
^-- SC1073 (error): Couldn't parse this for loop. Fix to allow more checks.
           ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
           ^-- SC1058 (error): Expected 'do'.
           ^-- SC1072 (error): Expected 'do'. Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1058 -- Expected 'do'.
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1072 -- Expected 'do'. Fix any mentioned ...

ShellCheck results for .\modules\nf-core\gem2\gem2bedmappability\main.nf:

In .\modules\nf-core\gem2\gem2bedmappability\main.nf line 28:

    --input ${map} \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "${map}" \

In .\modules\nf-core\gem2\gem2bedmappability\main.nf line 29:

    --index ${index} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --index "${index}" \

In .\modules\nf-core\gem2\gem2bedmappability\main.nf line 30:

    --output ${prefix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gem2\gemindexer\main.nf:

In .\modules\nf-core\gem2\gemindexer\main.nf line 28:

    -i ${fasta} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${fasta}" \

In .\modules\nf-core\gem2\gemindexer\main.nf line 29:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\gem2\gemindexer\main.nf line 30:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\gem2\gemindexer\main.nf line 32:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gem2\gemmappability\main.nf:

In .\modules\nf-core\gem2\gemmappability\main.nf line 28:

    -I ${index} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -I "${index}" \

In .\modules\nf-core\gem2\gemmappability\main.nf line 29:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\gem2\gemmappability\main.nf line 30:

    -l ${read_length} \
       ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -l "${read_length}" \

In .\modules\nf-core\gem2\gemmappability\main.nf line 31:

    -T ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -T "${task.cpus}" \

In .\modules\nf-core\gem2\gemmappability\main.nf line 32:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gem3\gem3indexer\main.nf:

In .\modules\nf-core\gem3\gem3indexer\main.nf line 28:

    -i ${fasta} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${fasta}" \

In .\modules\nf-core\gem3\gem3indexer\main.nf line 29:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\gem3\gem3indexer\main.nf line 30:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\gem3\gem3indexer\main.nf line 31:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gem3\gem3mapper\main.nf:

In .\modules\nf-core\gem3\gem3mapper\main.nf line 28:

gem-mapper -F 'SAM' -I $gem -i $fastq -t $task.cpus $args | samtools $samtools_command $args2 -@ $task.cpus -o ${prefix}.bam -
                       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.
                               ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                         ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                     ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                                               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gem-mapper -F 'SAM' -I "$gem" -i "$fastq" -t "$task".cpus "$args" | samtools "$samtools_command" "$args2" -@ "$task".cpus -o "${prefix}".bam -

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\genescopefk\main.nf:

In .\modules\nf-core\genescopefk\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\genescopefk\main.nf line 36:

    --input $fastk_histex_histogram \
            ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$fastk_histex_histogram" \

In .\modules\nf-core\genescopefk\main.nf line 38:

    --name_prefix ${prefix}
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --name_prefix "${prefix}"

In .\modules\nf-core\genescopefk\main.nf line 40:

printf -v KMERCOV "%.2f" \$( grep "^kmercov" *_model.txt | cut -d" " -f2 )
          ^-----^ SC2034 (warning): KMERCOV appears unused. Verify use (or export if used externally).
                           ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
                           ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- KMERCOV appears unused. Verify us...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...

ShellCheck results for .\modules\nf-core\genmap\index\main.nf:

In .\modules\nf-core\genmap\index\main.nf line 27:

    --fasta-file ${fasta} \
                 ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fasta-file "${fasta}" \

In .\modules\nf-core\genmap\index\main.nf line 28:

    --index ${prefix} \
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --index "${prefix}" \

In .\modules\nf-core\genmap\index\main.nf line 29:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\genmap\map\main.nf:

In .\modules\nf-core\genmap\map\main.nf line 33:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\genmap\map\main.nf line 34:

    ${bed} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bed}" \

In .\modules\nf-core\genmap\map\main.nf line 35:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\genmap\map\main.nf line 36:

    --index ${index} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --index "${index}" \

In .\modules\nf-core\genmap\map\main.nf line 37:

    --output ${prefix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\genmod\annotate\main.nf:

In .\modules\nf-core\genmod\annotate\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\genmod\annotate\main.nf line 27:

    --outfile ${prefix}_annotate.vcf \
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outfile "${prefix}"_annotate.vcf \

In .\modules\nf-core\genmod\annotate\main.nf line 28:

    $input_vcf
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_vcf"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\genmod\compound\main.nf:

In .\modules\nf-core\genmod\compound\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\genmod\compound\main.nf line 27:

    --processes ${task.cpus} \
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --processes "${task.cpus}" \

In .\modules\nf-core\genmod\compound\main.nf line 28:

    --outfile ${prefix}_compound.vcf \
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outfile "${prefix}"_compound.vcf \

In .\modules\nf-core\genmod\compound\main.nf line 29:

    $input_vcf
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_vcf"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\genmod\models\main.nf:

In .\modules\nf-core\genmod\models\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\genmod\models\main.nf line 30:

    $pen_file \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$pen_file" \

In .\modules\nf-core\genmod\models\main.nf line 31:

    $family_file \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$family_file" \

In .\modules\nf-core\genmod\models\main.nf line 32:

    --processes ${task.cpus} \
                ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --processes "${task.cpus}" \

In .\modules\nf-core\genmod\models\main.nf line 33:

    --outfile ${prefix}_models.vcf \
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outfile "${prefix}"_models.vcf \

In .\modules\nf-core\genmod\models\main.nf line 34:

    $input_vcf
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_vcf"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\genmod\score\main.nf:

In .\modules\nf-core\genmod\score\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\genmod\score\main.nf line 30:

    $family_file \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$family_file" \

In .\modules\nf-core\genmod\score\main.nf line 31:

    $config_file \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$config_file" \

In .\modules\nf-core\genmod\score\main.nf line 32:

    --outfile ${prefix}_score.vcf \
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outfile "${prefix}"_score.vcf \

In .\modules\nf-core\genmod\score\main.nf line 33:

    $input_vcf
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_vcf"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\genomad\endtoend\main.nf:

In .\modules\nf-core\genomad\endtoend\main.nf line 39:

    $fasta \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" \

In .\modules\nf-core\genomad\endtoend\main.nf line 41:

    $genomad_db \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$genomad_db" \

In .\modules\nf-core\genomad\endtoend\main.nf line 42:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\genomad\endtoend\main.nf line 43:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\genomescope2\main.nf:

In .\modules\nf-core\genomescope2\main.nf line 32:

    --input $histogram \
            ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$histogram" \

In .\modules\nf-core\genomescope2\main.nf line 33:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\genomescope2\main.nf line 35:

    --name_prefix $prefix
                  ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --name_prefix "$prefix"

In .\modules\nf-core\genomescope2\main.nf line 37:

test -f "fitted_hist.png" && mv fitted_hist.png ${prefix}_fitted_hist.png
                                                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
test -f "fitted_hist.png" && mv fitted_hist.png "${prefix}"_fitted_hist.png

In .\modules\nf-core\genomescope2\main.nf line 38:

test -f "lookup_table.txt" && mv lookup_table.txt ${prefix}_lookup_table.txt
                                                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
test -f "lookup_table.txt" && mv lookup_table.txt "${prefix}"_lookup_table.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\genotyphi\parse\main.nf:

In .\modules\nf-core\genotyphi\parse\main.nf line 26:

    --jsons $json \
            ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --jsons "$json" \

In .\modules\nf-core\genotyphi\parse\main.nf line 27:

    --prefix ${prefix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --prefix "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\genrich\main.nf:

In .\modules\nf-core\genrich\main.nf line 43:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\genrich\main.nf line 44:

    $treatment \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$treatment" \

In .\modules\nf-core\genrich\main.nf line 45:

    $control \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$control" \

In .\modules\nf-core\genrich\main.nf line 46:

    $blacklist \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$blacklist" \

In .\modules\nf-core\genrich\main.nf line 47:

    -o ${prefix}.narrowPeak
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".narrowPeak

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\geofetch\main.nf:

In .\modules\nf-core\geofetch\main.nf line 24:

    $geo_accession \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$geo_accession" \

In .\modules\nf-core\geofetch\main.nf line 27:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\geoquery\getgeo\main.nf:

In .\modules\nf-core\geoquery\getgeo\main.nf line 28:

touch ${prefix}.rds
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".rds

In .\modules\nf-core\geoquery\getgeo\main.nf line 29:

touch ${prefix}.matrix.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".matrix.tsv

In .\modules\nf-core\geoquery\getgeo\main.nf line 30:

touch ${prefix}.annotation.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".annotation.tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\getorganelle\config\main.nf:

In .\modules\nf-core\getorganelle\config\main.nf line 24:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\getorganelle\config\main.nf line 25:

    -a ${organelle_type} \
       ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -a "${organelle_type}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\getorganelle\fromreads\main.nf:

In .\modules\nf-core\getorganelle\fromreads\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\getorganelle\fromreads\main.nf line 29:

    --prefix ${meta.id}. \
             ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --prefix "${meta.id}". \

In .\modules\nf-core\getorganelle\fromreads\main.nf line 30:

    -F $organelle_type \
       ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -F "$organelle_type" \

In .\modules\nf-core\getorganelle\fromreads\main.nf line 31:

    --config-dir $db \
                 ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --config-dir "$db" \

In .\modules\nf-core\getorganelle\fromreads\main.nf line 32:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\getorganelle\fromreads\main.nf line 33:

    -1 ${fastq[0]} \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -1 "${fastq[0]}" \

In .\modules\nf-core\getorganelle\fromreads\main.nf line 34:

    -2 ${fastq[1]} \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -2 "${fastq[1]}" \

In .\modules\nf-core\getorganelle\fromreads\main.nf line 38:

    cp results/${prefix}.${organelle_type}*graph1.1*fasta results/${prefix}.${organelle_type}.fasta
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                         ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                            ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    cp results/"${prefix}"."${organelle_type}"*graph1.1*fasta results/"${prefix}"."${organelle_type}".fasta

In .\modules\nf-core\getorganelle\fromreads\main.nf line 39:

    gzip results/${prefix}.${organelle_type}.fasta
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                           ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip results/"${prefix}"."${organelle_type}".fasta

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gfaffix\main.nf:

In .\modules\nf-core\gfaffix\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gfaffix\main.nf line 28:

    $gfa \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gfa" \

In .\modules\nf-core\gfaffix\main.nf line 29:

    -o ${prefix}.gfaffix.gfa > ${prefix}.affixes.txt
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".gfaffix.gfa > "${prefix}".affixes.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gfastats\main.nf:

In .\modules\nf-core\gfastats\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gfastats\main.nf line 39:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\gfastats\main.nf line 40:

    $agp \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$agp" \

In .\modules\nf-core\gfastats\main.nf line 41:

    $ibed \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ibed" \

In .\modules\nf-core\gfastats\main.nf line 42:

    $ebed \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ebed" \

In .\modules\nf-core\gfastats\main.nf line 43:

    $sak \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sak" \

In .\modules\nf-core\gfastats\main.nf line 44:

    $output_sequences \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$output_sequences" \

In .\modules\nf-core\gfastats\main.nf line 45:

    --input-sequence $assembly \
                     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input-sequence "$assembly" \

In .\modules\nf-core\gfastats\main.nf line 46:

    $genome_size \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$genome_size" \

In .\modules\nf-core\gfastats\main.nf line 47:

    $target \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$target" \

In .\modules\nf-core\gfastats\main.nf line 48:

    > ${prefix}.assembly_summary
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".assembly_summary

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gfatools\gfa2fa\main.nf:

In .\modules\nf-core\gfatools\gfa2fa\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gfatools\gfa2fa\main.nf line 27:

    $gfa \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gfa" \

In .\modules\nf-core\gfatools\gfa2fa\main.nf line 28:

    | gzip -c > ${prefix}.fasta.gz
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | gzip -c > "${prefix}".fasta.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gfatools\stat\main.nf:

In .\modules\nf-core\gfatools\stat\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gfatools\stat\main.nf line 27:

    $gfa \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gfa" \

In .\modules\nf-core\gfatools\stat\main.nf line 28:

    > ${prefix}.stats
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".stats

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gffcompare\main.nf:

In .\modules\nf-core\gffcompare\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gffcompare\main.nf line 36:

    $ref_fasta \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ref_fasta" \

In .\modules\nf-core\gffcompare\main.nf line 37:

    $ref_gtf \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ref_gtf" \

In .\modules\nf-core\gffcompare\main.nf line 38:

    -o $prefix \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "$prefix" \

In .\modules\nf-core\gffcompare\main.nf line 39:

    $gtfs
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gtfs"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gffread\main.nf:

In .\modules\nf-core\gffread\main.nf line 35:

    $gff \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gff" \

In .\modules\nf-core\gffread\main.nf line 36:

    $fasta_arg \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta_arg" \

In .\modules\nf-core\gffread\main.nf line 37:

    $args_sorted \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args_sorted" \

In .\modules\nf-core\gffread\main.nf line 38:

    $output
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$output"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gget\gget\main.nf:

In .\modules\nf-core\gget\gget\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gget\gget\main.nf line 31:

    -o ${prefix}.${extension} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}"."${extension}" \

In .\modules\nf-core\gget\gget\main.nf line 32:

    $inputs
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$inputs"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\glimpse\chunk\main.nf:

In .\modules\nf-core\glimpse\chunk\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\glimpse\chunk\main.nf line 27:

    --input $input \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$input" \

In .\modules\nf-core\glimpse\chunk\main.nf line 28:

    --region $region \
             ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --region "$region" \

In .\modules\nf-core\glimpse\chunk\main.nf line 29:

    --thread $task.cpus \
             ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --thread "$task".cpus \

In .\modules\nf-core\glimpse\chunk\main.nf line 30:

    --output ${prefix}.txt
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\glimpse\concordance\main.nf:

In .\modules\nf-core\glimpse\concordance\main.nf line 34:

echo $region $freq $truth $estimate > input.txt
     ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
             ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                   ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
echo "$region" "$freq" "$truth" "$estimate" > input.txt

In .\modules\nf-core\glimpse\concordance\main.nf line 36:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\glimpse\concordance\main.nf line 38:

    --thread $task.cpus \
             ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --thread "$task".cpus \

In .\modules\nf-core\glimpse\concordance\main.nf line 39:

    --output ${prefix} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}" \

In .\modules\nf-core\glimpse\concordance\main.nf line 40:

    $min_prob_cmd \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$min_prob_cmd" \

In .\modules\nf-core\glimpse\concordance\main.nf line 41:

    $min_dp_cmd \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$min_dp_cmd" \

In .\modules\nf-core\glimpse\concordance\main.nf line 42:

    $bins_cmd
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bins_cmd"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\glimpse\ligate\main.nf:

In .\modules\nf-core\glimpse\ligate\main.nf line 25:

printf "%s\n" $input_list | tr -d '[],' > all_files.txt
              ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
printf "%s\n" "$input_list" | tr -d '[],' > all_files.txt

In .\modules\nf-core\glimpse\ligate\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\glimpse\ligate\main.nf line 30:

    --thread $task.cpus \
             ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --thread "$task".cpus \

In .\modules\nf-core\glimpse\ligate\main.nf line 31:

    --output ${prefix}.${suffix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${suffix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\glimpse\phase\main.nf:

In .\modules\nf-core\glimpse\phase\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\glimpse\phase\main.nf line 31:

    --input $input \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$input" \

In .\modules\nf-core\glimpse\phase\main.nf line 32:

    --reference $reference \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$reference" \

In .\modules\nf-core\glimpse\phase\main.nf line 33:

    $map_command \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$map_command" \

In .\modules\nf-core\glimpse\phase\main.nf line 34:

    $samples_file_command \
    ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$samples_file_command" \

In .\modules\nf-core\glimpse\phase\main.nf line 35:

    --input-region $input_region \
                   ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input-region "$input_region" \

In .\modules\nf-core\glimpse\phase\main.nf line 36:

    --output-region $output_region \
                    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-region "$output_region" \

In .\modules\nf-core\glimpse\phase\main.nf line 37:

    --thread $task.cpus \
             ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --thread "$task".cpus \

In .\modules\nf-core\glimpse\phase\main.nf line 38:

    --output ${prefix}.${suffix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${suffix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\glimpse\sample\main.nf:

In .\modules\nf-core\glimpse\sample\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\glimpse\sample\main.nf line 28:

    --input $input \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$input" \

In .\modules\nf-core\glimpse\sample\main.nf line 29:

    --thread $task.cpus \
             ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --thread "$task".cpus \

In .\modules\nf-core\glimpse\sample\main.nf line 30:

    --output ${prefix}.${suffix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${suffix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\glimpse2\chunk\main.nf:

In .\modules\nf-core\glimpse2\chunk\main.nf line 37:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\glimpse2\chunk\main.nf line 38:

    $map_cmd \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$map_cmd" \

In .\modules\nf-core\glimpse2\chunk\main.nf line 39:

    --${model} \
      ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --"${model}" \

In .\modules\nf-core\glimpse2\chunk\main.nf line 40:

    --input $input \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input "$input" \

In .\modules\nf-core\glimpse2\chunk\main.nf line 41:

    --region $region \
             ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --region "$region" \

In .\modules\nf-core\glimpse2\chunk\main.nf line 42:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\glimpse2\chunk\main.nf line 43:

    --output ${prefix}.txt
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\glimpse2\concordance\main.nf:

In .\modules\nf-core\glimpse2\concordance\main.nf line 45:

printf '$region_str' > regions.txt
       ^-----------^ SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\glimpse2\concordance\main.nf line 46:

sed 's/\$/ $freq $truth $estimate/' regions.txt > input.txt
    ^-----------------------------^ SC2016 (info): Expressions don't expand in single quotes, use double quotes for that.

In .\modules\nf-core\glimpse2\concordance\main.nf line 48:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\glimpse2\concordance\main.nf line 49:

    $samples_cmd \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$samples_cmd" \

In .\modules\nf-core\glimpse2\concordance\main.nf line 50:

    $groups_cmd \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$groups_cmd" \

In .\modules\nf-core\glimpse2\concordance\main.nf line 51:

    $bins_cmd \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bins_cmd" \

In .\modules\nf-core\glimpse2\concordance\main.nf line 52:

    $ac_bins_cmd \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ac_bins_cmd" \

In .\modules\nf-core\glimpse2\concordance\main.nf line 53:

    $ale_ct_cmd \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ale_ct_cmd" \

In .\modules\nf-core\glimpse2\concordance\main.nf line 54:

    $min_val_gl_cmd \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$min_val_gl_cmd" \

In .\modules\nf-core\glimpse2\concordance\main.nf line 55:

    $min_val_dp_cmd \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$min_val_dp_cmd" \

In .\modules\nf-core\glimpse2\concordance\main.nf line 57:

    --thread $task.cpus \
             ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --thread "$task".cpus \

In .\modules\nf-core\glimpse2\concordance\main.nf line 58:

    --output ${prefix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2016 -- Expressions don't expand in singl...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\glimpse2\ligate\main.nf:

In .\modules\nf-core\glimpse2\ligate\main.nf line 25:

printf "%s\n" $input_list | tr -d '[],' | sort -V > all_files.txt
              ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
printf "%s\n" "$input_list" | tr -d '[],' | sort -V > all_files.txt

In .\modules\nf-core\glimpse2\ligate\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\glimpse2\ligate\main.nf line 30:

    --thread $task.cpus \
             ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --thread "$task".cpus \

In .\modules\nf-core\glimpse2\ligate\main.nf line 31:

    --output ${prefix}.${suffix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${suffix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\glimpse2\phase\main.nf:

In .\modules\nf-core\glimpse2\phase\main.nf line 66:

    ls -1 | grep '\.cram\$\|\.bam\$' > all_bam.txt
    ^-- SC2010 (warning): Don't use ls | grep. Use a glob or a for loop with a condition to allow non-alphanumeric filenames.

In .\modules\nf-core\glimpse2\phase\main.nf line 74:

        input_command="--input-gl $input"
        ^-----------^ SC2034 (warning): input_command appears unused. Verify use (or export if used externally).

In .\modules\nf-core\glimpse2\phase\main.nf line 83:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\glimpse2\phase\main.nf line 85:

    --reference $reference \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$reference" \

In .\modules\nf-core\glimpse2\phase\main.nf line 86:

    $map_command \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$map_command" \

In .\modules\nf-core\glimpse2\phase\main.nf line 87:

    $fasta_command \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta_command" \

In .\modules\nf-core\glimpse2\phase\main.nf line 88:

    $samples_file_command \
    ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$samples_file_command" \

In .\modules\nf-core\glimpse2\phase\main.nf line 89:

    $input_region_cmd \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input_region_cmd" \

In .\modules\nf-core\glimpse2\phase\main.nf line 90:

    $output_region_cmd \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$output_region_cmd" \

In .\modules\nf-core\glimpse2\phase\main.nf line 91:

    --thread $task.cpus \
             ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --thread "$task".cpus \

In .\modules\nf-core\glimpse2\phase\main.nf line 92:

    --output ${prefix}.${suffix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"."${suffix}"

For more information:
  https://www.shellcheck.net/wiki/SC2010 -- Don't use ls | grep. Use a glob o...
  https://www.shellcheck.net/wiki/SC2034 -- input_command appears unused. Ver...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\glimpse2\splitreference\main.nf:

In .\modules\nf-core\glimpse2\splitreference\main.nf line 39:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\glimpse2\splitreference\main.nf line 40:

    --reference $reference \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$reference" \

In .\modules\nf-core\glimpse2\splitreference\main.nf line 41:

    $map_command \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$map_command" \

In .\modules\nf-core\glimpse2\splitreference\main.nf line 42:

    --input-region $input_region \
                   ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input-region "$input_region" \

In .\modules\nf-core\glimpse2\splitreference\main.nf line 43:

    --output-region $output_region \
                    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-region "$output_region" \

In .\modules\nf-core\glimpse2\splitreference\main.nf line 44:

    --thread $task.cpus \
             ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --thread "$task".cpus \

In .\modules\nf-core\glimpse2\splitreference\main.nf line 45:

    --output ${prefix}
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\glnexus\main.nf:

In .\modules\nf-core\glnexus\main.nf line 36:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\glnexus\main.nf line 37:

    --mem-gbytes $avail_mem \
                 ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --mem-gbytes "$avail_mem" \

In .\modules\nf-core\glnexus\main.nf line 38:

    $regions \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$regions" \

In .\modules\nf-core\glnexus\main.nf line 39:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\glnexus\main.nf line 40:

    ${input.join(' ')} \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input.join(' ')}" \

In .\modules\nf-core\glnexus\main.nf line 41:

    > ${prefix}.bcf
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bcf

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gmmdemux\main.nf:

In .\modules\nf-core\gmmdemux\main.nf line 40:

    cat /dev/null > ${prefix}_summary_report.txt
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    cat /dev/null > "${prefix}"_summary_report.txt

In .\modules\nf-core\gmmdemux\main.nf line 43:

GMM-demux $args \
          ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
GMM-demux "$args" \

In .\modules\nf-core\gmmdemux\main.nf line 44:

    $type_report \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$type_report" \

In .\modules\nf-core\gmmdemux\main.nf line 45:

    $summary_rep \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$summary_rep" \

In .\modules\nf-core\gmmdemux\main.nf line 46:

    $skip \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$skip" \

In .\modules\nf-core\gmmdemux\main.nf line 47:

    $examine_cells \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$examine_cells" \

In .\modules\nf-core\gmmdemux\main.nf line 48:

    $hto_matrix \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$hto_matrix" \

In .\modules\nf-core\gmmdemux\main.nf line 49:

    $hto_names \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$hto_names" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gnu\sort\main.nf:

In .\modules\nf-core\gnu\sort\main.nf line 28:

sort ${args} ${input} > ${output_file}
     ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
             ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
sort "${args}" "${input}" > "${output_file}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gnu\split\main.nf:

In .\modules\nf-core\gnu\split\main.nf line 27:

gunzip -c ${input} | split ${args} --additional-suffix=.${next_suffix} - ${prefix}.split.
          ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                           ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                        ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gunzip -c "${input}" | split "${args}" --additional-suffix=."${next_suffix}" - "${prefix}".split.

In .\modules\nf-core\gnu\split\main.nf line 28:

gzip ${prefix}.split.*
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip "${prefix}".split.*

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\goat\taxonsearch\main.nf:

In .\modules\nf-core\goat\taxonsearch\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\goat\taxonsearch\main.nf line 29:

    $input > ${prefix}.tsv
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input" > "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\goleft\indexcov\main.nf:

In .\modules\nf-core\goleft\indexcov\main.nf line 35:

    --fai ${fai}  \
          ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fai "${fai}"  \

In .\modules\nf-core\goleft\indexcov\main.nf line 36:

    --directory ${prefix} \
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --directory "${prefix}" \

In .\modules\nf-core\goleft\indexcov\main.nf line 37:

    ${extranormalize} \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${extranormalize}" \

In .\modules\nf-core\goleft\indexcov\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\goleft\indexcov\main.nf line 39:

    ${input_files.join(" ")}
    ^----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_files.join(" ")}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\goleft\indexsplit\main.nf:

In .\modules\nf-core\goleft\indexsplit\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\goleft\indexsplit\main.nf line 29:

    -n ${split} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -n "${split}" \

In .\modules\nf-core\goleft\indexsplit\main.nf line 30:

    --fai ${fai} \
          ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fai "${fai}" \

In .\modules\nf-core\goleft\indexsplit\main.nf line 31:

    ${bai} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bai}" \

In .\modules\nf-core\goleft\indexsplit\main.nf line 32:

    > ${prefix}.bed
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gprofiler2\gost\main.nf:

In .\modules\nf-core\gprofiler2\gost\main.nf line 35:

touch ${prefix}.gprofiler2.all_enriched_pathways.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".gprofiler2.all_enriched_pathways.tsv

In .\modules\nf-core\gprofiler2\gost\main.nf line 36:

touch ${prefix}.gprofiler2.gost_results.rds
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".gprofiler2.gost_results.rds

In .\modules\nf-core\gprofiler2\gost\main.nf line 37:

touch ${prefix}.gprofiler2.gostplot.png
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".gprofiler2.gostplot.png

In .\modules\nf-core\gprofiler2\gost\main.nf line 38:

touch ${prefix}.gprofiler2.gostplot.html
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".gprofiler2.gostplot.html

In .\modules\nf-core\gprofiler2\gost\main.nf line 39:

touch ${prefix}.gprofiler2.*.sub_enriched_pathways.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".gprofiler2.*.sub_enriched_pathways.tsv

In .\modules\nf-core\gprofiler2\gost\main.nf line 40:

touch ${prefix}.gprofiler2.*.sub_enriched_pathways.png
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".gprofiler2.*.sub_enriched_pathways.png

In .\modules\nf-core\gprofiler2\gost\main.nf line 41:

touch ${prefix}.ENSG_filtered.gmt
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".ENSG_filtered.gmt

In .\modules\nf-core\gprofiler2\gost\main.nf line 42:

touch ${prefix}.R_sessionInfo.log
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".R_sessionInfo.log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\grabix\check\main.nf:

In .\modules\nf-core\grabix\check\main.nf line 23:

grabix check ${input} | tr -d '\n'
             ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
grabix check "${input}" | tr -d '\n'

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\graphmap2\align\main.nf:

In .\modules\nf-core\graphmap2\align\main.nf line 29:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\graphmap2\align\main.nf line 30:

    -r $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -r "$fasta" \

In .\modules\nf-core\graphmap2\align\main.nf line 31:

    -i $index \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$index" \

In .\modules\nf-core\graphmap2\align\main.nf line 32:

    -d $reads \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -d "$reads" \

In .\modules\nf-core\graphmap2\align\main.nf line 33:

    -o ${prefix}.sam \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".sam \

In .\modules\nf-core\graphmap2\align\main.nf line 34:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\graphmap2\index\main.nf:

In .\modules\nf-core\graphmap2\index\main.nf line 24:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\graphmap2\index\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\graphmap2\index\main.nf line 27:

    -r $fasta
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -r "$fasta"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\graphtyper\genotype\main.nf:

In .\modules\nf-core\graphtyper\genotype\main.nf line 32:

printf "$bam_path_text" > bam_list.txt
       ^--------------^ SC2059 (info): Don't use variables in the printf format string. Use printf '..%s..' "$foo".

In .\modules\nf-core\graphtyper\genotype\main.nf line 35:

    $ref \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ref" \

In .\modules\nf-core\graphtyper\genotype\main.nf line 36:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\graphtyper\genotype\main.nf line 38:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\graphtyper\genotype\main.nf line 39:

    $region_text
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$region_text"

For more information:
  https://www.shellcheck.net/wiki/SC2059 -- Don't use variables in the printf...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\graphtyper\vcfconcatenate\main.nf:

In .\modules\nf-core\graphtyper\vcfconcatenate\main.nf line 37:

    ${prefix}_subset_*.vcf.gz \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"_subset_*.vcf.gz \

In .\modules\nf-core\graphtyper\vcfconcatenate\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\graphtyper\vcfconcatenate\main.nf line 40:

    --output=${prefix}.vcf.gz
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output="${prefix}".vcf.gz

In .\modules\nf-core\graphtyper\vcfconcatenate\main.nf line 43:

rm ${prefix}_subset_*.vcf.gz
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
rm "${prefix}"_subset_*.vcf.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gridss\generateponbedpe\main.nf:

In .\modules\nf-core\gridss\generateponbedpe\main.nf line 35:

    ${vcf_command} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${vcf_command}" \

In .\modules\nf-core\gridss\generateponbedpe\main.nf line 36:

    ${bedpe_command} \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bedpe_command}" \

In .\modules\nf-core\gridss\generateponbedpe\main.nf line 37:

    ${bed_command} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bed_command}" \

In .\modules\nf-core\gridss\generateponbedpe\main.nf line 38:

    ${ref} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${ref}" \

In .\modules\nf-core\gridss\generateponbedpe\main.nf line 39:

    OUTPUT_BEDPE=${prefix}.bedpe \
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    OUTPUT_BEDPE="${prefix}".bedpe \

In .\modules\nf-core\gridss\generateponbedpe\main.nf line 40:

    OUTPUT_BED=${prefix}.bed \
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    OUTPUT_BED="${prefix}".bed \

In .\modules\nf-core\gridss\generateponbedpe\main.nf line 41:

    THREADS=$task.cpus \
            ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    THREADS="$task".cpus \

In .\modules\nf-core\gridss\generateponbedpe\main.nf line 42:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gridss\gridss\main.nf:

In .\modules\nf-core\gridss\gridss\main.nf line 34:

    --output ${prefix}.vcf.gz \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output "${prefix}".vcf.gz \

In .\modules\nf-core\gridss\gridss\main.nf line 35:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\gridss\gridss\main.nf line 36:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\gridss\gridss\main.nf line 37:

    --jvmheap ${task.memory.toGiga() - 1}g \
              ^-------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --jvmheap "${task.memory.toGiga() - 1}"g \

In .\modules\nf-core\gridss\gridss\main.nf line 38:

    --otherjvmheap ${task.memory.toGiga() - 1}g \
                   ^-------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --otherjvmheap "${task.memory.toGiga() - 1}"g \

In .\modules\nf-core\gridss\gridss\main.nf line 39:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gridss\gridss\main.nf line 40:

    ${inputs}
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${inputs}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gridss\somaticfilter\main.nf:

In .\modules\nf-core\gridss\somaticfilter\main.nf line 40:

SCRIPT_PATH=\$(find / -name libgridss.R 2>/dev/null | head -n 1)
^---------^ SC2034 (warning): SCRIPT_PATH appears unused. Verify use (or export if used externally).
              ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
              ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- SCRIPT_PATH appears unused. Verif...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1088 -- Parsing stopped here. Invalid use...

ShellCheck results for .\modules\nf-core\gsea\gsea\main.nf:

In .\modules\nf-core\gsea\gsea\main.nf line 53:

    -res $gct \
         ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -res "$gct" \

In .\modules\nf-core\gsea\gsea\main.nf line 54:

    -cls ${cls}#${target}_versus_${reference} \
         ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -cls "${cls}"#"${target}"_versus_"${reference}" \

In .\modules\nf-core\gsea\gsea\main.nf line 55:

    -gmx $gene_sets \
         ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -gmx "$gene_sets" \

In .\modules\nf-core\gsea\gsea\main.nf line 56:

    $chip_command \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$chip_command" \

In .\modules\nf-core\gsea\gsea\main.nf line 58:

    --rpt_label $rpt_label \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --rpt_label "$rpt_label" \

In .\modules\nf-core\gsea\gsea\main.nf line 59:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

In .\modules\nf-core\gsea\gsea\main.nf line 62:

mv ${rpt_label}.Gsea.*/* .
   ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${rpt_label}".Gsea.*/* .

In .\modules\nf-core\gsea\gsea\main.nf line 63:

timestamp=\$(cat *.rpt | grep producer_timestamp | awk '{print \$2}')
^-------^ SC2034 (warning): timestamp appears unused. Verify use (or export if used externally).
            ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
            ^-- SC1088 (error): Parsing stopped here. Invalid use of parentheses?

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- timestamp appears unused. Verify ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...

ShellCheck results for .\modules\nf-core\gstama\collapse\main.nf:

In .\modules\nf-core\gstama\collapse\main.nf line 35:

    -s $bam \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -s "$bam" \

In .\modules\nf-core\gstama\collapse\main.nf line 36:

    -f $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -f "$fasta" \

In .\modules\nf-core\gstama\collapse\main.nf line 37:

    -p ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${prefix}" \

In .\modules\nf-core\gstama\collapse\main.nf line 38:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gstama\merge\main.nf:

In .\modules\nf-core\gstama\merge\main.nf line 29:

    -f $filelist \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -f "$filelist" \

In .\modules\nf-core\gstama\merge\main.nf line 31:

    -p ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${prefix}" \

In .\modules\nf-core\gstama\merge\main.nf line 32:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gstama\polyacleanup\main.nf:

In .\modules\nf-core\gstama\polyacleanup\main.nf line 28:

    -f $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -f "$fasta" \

In .\modules\nf-core\gstama\polyacleanup\main.nf line 29:

    -p ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${prefix}" \

In .\modules\nf-core\gstama\polyacleanup\main.nf line 30:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

In .\modules\nf-core\gstama\polyacleanup\main.nf line 31:

gzip ${prefix}.fa
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip "${prefix}".fa

In .\modules\nf-core\gstama\polyacleanup\main.nf line 32:

gzip ${prefix}_polya_flnc_report.txt
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip "${prefix}"_polya_flnc_report.txt

In .\modules\nf-core\gstama\polyacleanup\main.nf line 33:

gzip ${prefix}_tails.fa
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip "${prefix}"_tails.fa

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gt\gff3\main.nf:

In .\modules\nf-core\gt\gff3\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gt\ltrharvest\main.nf:

In .\modules\nf-core\gt\ltrharvest\main.nf line 33:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gt\stat\main.nf:

In .\modules\nf-core\gt\stat\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gt\stat\main.nf line 27:

    $gff3 \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gff3" \

In .\modules\nf-core\gt\stat\main.nf line 28:

    > ${prefix}.yml
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".yml

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gt\suffixerator\main.nf:

In .\modules\nf-core\gt\suffixerator\main.nf line 32:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gt\suffixerator\main.nf line 33:

    -db $fasta \
        ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -db "$fasta" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gtdbtk\classifywf\main.nf:

In .\modules\nf-core\gtdbtk\classifywf\main.nf line 45:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\gtdbtk\classifywf\main.nf line 48:

    --out_dir ${prefix} \
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --out_dir "${prefix}" \

In .\modules\nf-core\gtdbtk\classifywf\main.nf line 49:

    --cpus ${task.cpus} \
           ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpus "${task.cpus}" \

In .\modules\nf-core\gtdbtk\classifywf\main.nf line 50:

    ${mash_mode} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${mash_mode}" \

In .\modules\nf-core\gtdbtk\classifywf\main.nf line 51:

    ${pplacer_scratch}
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${pplacer_scratch}"

In .\modules\nf-core\gtdbtk\classifywf\main.nf line 53:

mv ${prefix}/gtdbtk.log "${prefix}/${prefix}.log"
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${prefix}"/gtdbtk.log "${prefix}/${prefix}.log"

In .\modules\nf-core\gtdbtk\classifywf\main.nf line 54:

mv ${prefix}/gtdbtk.warnings.log "${prefix}/${prefix}.warnings.log"
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${prefix}"/gtdbtk.warnings.log "${prefix}/${prefix}.warnings.log"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gtdbtk\gtdbtoncbimajorityvote\main.nf:

In .\modules\nf-core\gtdbtk\gtdbtoncbimajorityvote\main.nf line 33:

    --gtdbtk_output_dir ${gtdbtk_outdir} \
                        ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --gtdbtk_output_dir "${gtdbtk_outdir}" \

In .\modules\nf-core\gtdbtk\gtdbtoncbimajorityvote\main.nf line 34:

    ${prefix_arg} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix_arg}" \

In .\modules\nf-core\gtdbtk\gtdbtoncbimajorityvote\main.nf line 35:

    ${bac120} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bac120}" \

In .\modules\nf-core\gtdbtk\gtdbtoncbimajorityvote\main.nf line 36:

    ${ar53} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${ar53}" \

In .\modules\nf-core\gtdbtk\gtdbtoncbimajorityvote\main.nf line 37:

    --output_file ${prefix}.ncbi.tsv \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output_file "${prefix}".ncbi.tsv \

In .\modules\nf-core\gtdbtk\gtdbtoncbimajorityvote\main.nf line 38:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gtfsort\main.nf:

In .\modules\nf-core\gtfsort\main.nf line 27:

    -i $gtf \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$gtf" \

In .\modules\nf-core\gtfsort\main.nf line 28:

    -o ${prefix}.sorted.gtf \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".sorted.gtf \

In .\modules\nf-core\gtfsort\main.nf line 29:

    -t $task.cpus
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gubbins\main.nf:

In .\modules\nf-core\gubbins\main.nf line 34:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\gubbins\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gubbins\main.nf line 36:

    $alignment
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$alignment"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gunc\downloaddb\main.nf:

In .\modules\nf-core\gunc\downloaddb\main.nf line 23:

gunc download_db . -db $db_name $args
                       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gunc download_db . -db "$db_name" "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gunc\mergecheckm\main.nf:

In .\modules\nf-core\gunc\mergecheckm\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gunc\mergecheckm\main.nf line 27:

    -g $gunc_file \
       ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$gunc_file" \

In .\modules\nf-core\gunc\mergecheckm\main.nf line 28:

    -c $checkm_file \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -c "$checkm_file" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gunc\run\main.nf:

In .\modules\nf-core\gunc\run\main.nf line 30:

    --db_file $db \
              ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --db_file "$db" \

In .\modules\nf-core\gunc\run\main.nf line 31:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\gunc\run\main.nf line 32:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gunzip\main.nf:

In .\modules\nf-core\gunzip\main.nf line 32:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\gunzip\main.nf line 33:

    ${archive} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${archive}" \

In .\modules\nf-core\gunzip\main.nf line 34:

    > ${gunzip}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${gunzip}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gvcftools\extractvariants\main.nf:

In .\modules\nf-core\gvcftools\extractvariants\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\gvcftools\extractvariants\main.nf line 29:

    $gvcf |
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gvcf" |

In .\modules\nf-core\gvcftools\extractvariants\main.nf line 30:

gzip -c > ${prefix}.vcf.gz
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip -c > "${prefix}".vcf.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\gzrt\main.nf:

In .\modules\nf-core\gzrt\main.nf line 35:

if [ "$meta.single_end" == true ]; then
                        ^-- SC2193 (warning): The arguments to this comparison can never be equal. Make sure your syntax is correct.

In .\modules\nf-core\gzrt\main.nf line 36:

    gzrecover ${args} -p ${fastqgz} | gzip > ${prefix}.fastq.gz
              ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                         ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzrecover "${args}" -p "${fastqgz}" | gzip > "${prefix}".fastq.gz

In .\modules\nf-core\gzrt\main.nf line 39:

        echo "" | gzip > ${prefix}.fastq.gz
                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        echo "" | gzip > "${prefix}".fastq.gz

In .\modules\nf-core\gzrt\main.nf line 42:

    gzrecover ${args} -p ${fastqgz[0]} | gzip > ${prefix}_1.fastq.gz
              ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                         ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzrecover "${args}" -p "${fastqgz[0]}" | gzip > "${prefix}"_1.fastq.gz

In .\modules\nf-core\gzrt\main.nf line 43:

    gzrecover ${args} -p ${fastqgz[1]} | gzip > ${prefix}_2.fastq.gz
              ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                         ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzrecover "${args}" -p "${fastqgz[1]}" | gzip > "${prefix}"_2.fastq.gz

In .\modules\nf-core\gzrt\main.nf line 46:

        echo "" | gzip > ${prefix}_1.fastq.gz
                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        echo "" | gzip > "${prefix}"_1.fastq.gz

In .\modules\nf-core\gzrt\main.nf line 50:

        echo "" | gzip > ${prefix}_2.fastq.gz
                         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        echo "" | gzip > "${prefix}"_2.fastq.gz

In .\modules\nf-core\gzrt\main.nf line 54:

soft_line="${task.process}"
^-------^ SC2034 (warning): soft_line appears unused. Verify use (or export if used externally).

In .\modules\nf-core\gzrt\main.nf line 55:

ver_line="gzrt: \$(gzrecover -V |& sed '1!d ; s/gzrecover //')"
^------^ SC2034 (warning): ver_line appears unused. Verify use (or export if used externally).

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- soft_line appears unused. Verify ...
  https://www.shellcheck.net/wiki/SC2193 -- The arguments to this comparison ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hamronization\abricate\main.nf:

In .\modules\nf-core\hamronization\abricate\main.nf line 30:

    ${report} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${report}" \

In .\modules\nf-core\hamronization\abricate\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hamronization\abricate\main.nf line 32:

    --format ${format} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --format "${format}" \

In .\modules\nf-core\hamronization\abricate\main.nf line 33:

    --analysis_software_version ${software_version} \
                                ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --analysis_software_version "${software_version}" \

In .\modules\nf-core\hamronization\abricate\main.nf line 34:

    --reference_database_version ${reference_db_version} \
                                 ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference_database_version "${reference_db_version}" \

In .\modules\nf-core\hamronization\abricate\main.nf line 35:

    > ${prefix}.${format}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${format}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hamronization\amrfinderplus\main.nf:

In .\modules\nf-core\hamronization\amrfinderplus\main.nf line 30:

    ${report} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${report}" \

In .\modules\nf-core\hamronization\amrfinderplus\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hamronization\amrfinderplus\main.nf line 32:

    --format ${format} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --format "${format}" \

In .\modules\nf-core\hamronization\amrfinderplus\main.nf line 33:

    --analysis_software_version ${software_version} \
                                ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --analysis_software_version "${software_version}" \

In .\modules\nf-core\hamronization\amrfinderplus\main.nf line 34:

    --reference_database_version ${reference_db_version} \
                                 ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference_database_version "${reference_db_version}" \

In .\modules\nf-core\hamronization\amrfinderplus\main.nf line 35:

    --input_file_name ${prefix} \
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input_file_name "${prefix}" \

In .\modules\nf-core\hamronization\amrfinderplus\main.nf line 36:

    > ${prefix}.${format}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${format}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hamronization\deeparg\main.nf:

In .\modules\nf-core\hamronization\deeparg\main.nf line 30:

    ${report} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${report}" \

In .\modules\nf-core\hamronization\deeparg\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hamronization\deeparg\main.nf line 32:

    --format ${format} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --format "${format}" \

In .\modules\nf-core\hamronization\deeparg\main.nf line 33:

    --analysis_software_version ${software_version} \
                                ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --analysis_software_version "${software_version}" \

In .\modules\nf-core\hamronization\deeparg\main.nf line 34:

    --reference_database_version ${reference_db_version} \
                                 ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference_database_version "${reference_db_version}" \

In .\modules\nf-core\hamronization\deeparg\main.nf line 35:

    --input_file_name ${prefix} \
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input_file_name "${prefix}" \

In .\modules\nf-core\hamronization\deeparg\main.nf line 36:

    > ${prefix}.${format}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${format}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hamronization\fargene\main.nf:

In .\modules\nf-core\hamronization\fargene\main.nf line 30:

    ${report} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${report}" \

In .\modules\nf-core\hamronization\fargene\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hamronization\fargene\main.nf line 32:

    --format ${format} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --format "${format}" \

In .\modules\nf-core\hamronization\fargene\main.nf line 33:

    --analysis_software_version ${software_version} \
                                ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --analysis_software_version "${software_version}" \

In .\modules\nf-core\hamronization\fargene\main.nf line 34:

    --reference_database_version ${reference_db_version} \
                                 ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference_database_version "${reference_db_version}" \

In .\modules\nf-core\hamronization\fargene\main.nf line 35:

    --input_file_name ${prefix} \
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input_file_name "${prefix}" \

In .\modules\nf-core\hamronization\fargene\main.nf line 36:

    > ${prefix}.${format}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${format}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hamronization\rgi\main.nf:

In .\modules\nf-core\hamronization\rgi\main.nf line 30:

    ${report} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${report}" \

In .\modules\nf-core\hamronization\rgi\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hamronization\rgi\main.nf line 32:

    --format ${format} \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --format "${format}" \

In .\modules\nf-core\hamronization\rgi\main.nf line 33:

    --analysis_software_version ${software_version} \
                                ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --analysis_software_version "${software_version}" \

In .\modules\nf-core\hamronization\rgi\main.nf line 34:

    --reference_database_version ${reference_db_version} \
                                 ^---------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference_database_version "${reference_db_version}" \

In .\modules\nf-core\hamronization\rgi\main.nf line 35:

    --input_file_name ${prefix} \
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input_file_name "${prefix}" \

In .\modules\nf-core\hamronization\rgi\main.nf line 36:

    > ${prefix}.${format}
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}"."${format}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hamronization\summarize\main.nf:

In .\modules\nf-core\hamronization\summarize\main.nf line 28:

    ${reports.join(' ')} \
    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reports.join(' ')}" \

In .\modules\nf-core\hamronization\summarize\main.nf line 29:

    -t ${format} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "${format}" \

In .\modules\nf-core\hamronization\summarize\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hamronization\summarize\main.nf line 31:

    -o hamronization_combined_report.${outformat}
                                     ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o hamronization_combined_report."${outformat}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hapibd\main.nf:

In .\modules\nf-core\hapibd\main.nf line 38:

hap-ibd -Xmx${avail_mem}M \
            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
hap-ibd -Xmx"${avail_mem}"M \

In .\modules\nf-core\hapibd\main.nf line 39:

    gt=${vcf} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gt="${vcf}" \

In .\modules\nf-core\hapibd\main.nf line 40:

    map=${map} \
        ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    map="${map}" \

In .\modules\nf-core\hapibd\main.nf line 41:

    out=${prefix} \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    out="${prefix}" \

In .\modules\nf-core\hapibd\main.nf line 42:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hapibd\main.nf line 43:

    ${excludesamples_command}
    ^-----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${excludesamples_command}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\haplocheck\main.nf:

In .\modules\nf-core\haplocheck\main.nf line 25:

haplocheck --raw --out $prefix $vcf
                       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                               ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
haplocheck --raw --out "$prefix" "$vcf"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\haplogrep2\classify\main.nf:

In .\modules\nf-core\haplogrep2\classify\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\haplogrep2\classify\main.nf line 28:

    --in $inputfile \
         ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --in "$inputfile" \

In .\modules\nf-core\haplogrep2\classify\main.nf line 29:

    --out ${prefix}.txt \
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --out "${prefix}".txt \

In .\modules\nf-core\haplogrep2\classify\main.nf line 30:

    --format $format
             ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --format "$format"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\haplogrep3\classify\main.nf:

In .\modules\nf-core\haplogrep3\classify\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\haplogrep3\classify\main.nf line 27:

    --in $inputfile \
         ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --in "$inputfile" \

In .\modules\nf-core\haplogrep3\classify\main.nf line 28:

    --out ${prefix}.txt
          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --out "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\happy\ftxpy\main.nf:

In .\modules\nf-core\happy\ftxpy\main.nf line 33:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\happy\ftxpy\main.nf line 34:

    $regions \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$regions" \

In .\modules\nf-core\happy\ftxpy\main.nf line 35:

    $targets \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$targets" \

In .\modules\nf-core\happy\ftxpy\main.nf line 36:

    $bams \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bams" \

In .\modules\nf-core\happy\ftxpy\main.nf line 37:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\happy\ftxpy\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\happy\ftxpy\main.nf line 39:

    $vcf
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\happy\happy\main.nf:

In .\modules\nf-core\happy\happy\main.nf line 46:

    ${truth_vcf} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${truth_vcf}" \

In .\modules\nf-core\happy\happy\main.nf line 47:

    ${query_vcf} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${query_vcf}" \

In .\modules\nf-core\happy\happy\main.nf line 48:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\happy\happy\main.nf line 49:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\happy\happy\main.nf line 50:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\happy\happy\main.nf line 51:

    ${regions} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions}" \

In .\modules\nf-core\happy\happy\main.nf line 52:

    ${targets} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${targets}" \

In .\modules\nf-core\happy\happy\main.nf line 53:

    ${false_positives} \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${false_positives}" \

In .\modules\nf-core\happy\happy\main.nf line 54:

    ${stratification} \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${stratification}" \

In .\modules\nf-core\happy\happy\main.nf line 55:

    -o ${prefix}
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\happy\prepy\main.nf:

In .\modules\nf-core\happy\prepy\main.nf line 30:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\happy\prepy\main.nf line 31:

    $restrict_region \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$restrict_region" \

In .\modules\nf-core\happy\prepy\main.nf line 32:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\happy\prepy\main.nf line 33:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\happy\prepy\main.nf line 34:

    $vcf \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf" \

In .\modules\nf-core\happy\prepy\main.nf line 35:

    ${prefix}.vcf.gz
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".vcf.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\happy\sompy\main.nf:

In .\modules\nf-core\happy\sompy\main.nf line 39:

    ${truth_vcf} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${truth_vcf}" \

In .\modules\nf-core\happy\sompy\main.nf line 40:

    ${query_vcf} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${query_vcf}" \

In .\modules\nf-core\happy\sompy\main.nf line 41:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\happy\sompy\main.nf line 42:

    --reference ${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "${fasta}" \

In .\modules\nf-core\happy\sompy\main.nf line 43:

    ${regions} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions}" \

In .\modules\nf-core\happy\sompy\main.nf line 44:

    ${targets} \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${targets}" \

In .\modules\nf-core\happy\sompy\main.nf line 45:

    ${false_positives} \
    ^----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${false_positives}" \

In .\modules\nf-core\happy\sompy\main.nf line 46:

    ${ambiguous} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${ambiguous}" \

In .\modules\nf-core\happy\sompy\main.nf line 47:

    ${bams} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bams}" \

In .\modules\nf-core\happy\sompy\main.nf line 48:

    -o ${prefix}
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\helitronscanner\draw\main.nf:

In .\modules\nf-core\helitronscanner\draw\main.nf line 33:

    . "/usr/local/env-activate.sh"
      ^--------------------------^ SC1091 (info): Not following: /usr/local/env-activate.sh was not specified as input (see shellcheck -x).

In .\modules\nf-core\helitronscanner\draw\main.nf line 39:

    -Xmx${avail_mem}g \
        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${avail_mem}"g \

In .\modules\nf-core\helitronscanner\draw\main.nf line 40:

    -head_score $head \
                ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -head_score "$head" \

In .\modules\nf-core\helitronscanner\draw\main.nf line 41:

    -tail_score $tail \
                ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -tail_score "$tail" \

In .\modules\nf-core\helitronscanner\draw\main.nf line 42:

    -output ${prefix}.pairends \
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -output "${prefix}".pairends \

In .\modules\nf-core\helitronscanner\draw\main.nf line 43:

    ${args2}
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args2}"

In .\modules\nf-core\helitronscanner\draw\main.nf line 47:

    -Xmx${avail_mem}g \
        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${avail_mem}"g \

In .\modules\nf-core\helitronscanner\draw\main.nf line 48:

    -pscore ${prefix}.pairends \
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -pscore "${prefix}".pairends \

In .\modules\nf-core\helitronscanner\draw\main.nf line 49:

    -g $fasta \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -g "$fasta" \

In .\modules\nf-core\helitronscanner\draw\main.nf line 50:

    -output ${prefix}.draw \
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -output "${prefix}".draw \

In .\modules\nf-core\helitronscanner\draw\main.nf line 51:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

In .\modules\nf-core\helitronscanner\draw\main.nf line 53:

mv ${prefix}.draw.hel.fa \
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${prefix}".draw.hel.fa \

In .\modules\nf-core\helitronscanner\draw\main.nf line 54:

    ${prefix}.draw
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".draw

For more information:
  https://www.shellcheck.net/wiki/SC1091 -- Not following: /usr/local/env-act...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\helitronscanner\scan\main.nf:

In .\modules\nf-core\helitronscanner\scan\main.nf line 40:

    . "/usr/local/env-activate.sh"
      ^--------------------------^ SC1091 (info): Not following: /usr/local/env-activate.sh was not specified as input (see shellcheck -x).

In .\modules\nf-core\helitronscanner\scan\main.nf line 45:

    $subcommand \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$subcommand" \

In .\modules\nf-core\helitronscanner\scan\main.nf line 46:

    -Xmx${avail_mem}g \
        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -Xmx"${avail_mem}"g \

In .\modules\nf-core\helitronscanner\scan\main.nf line 47:

    $lcv_arg \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$lcv_arg" \

In .\modules\nf-core\helitronscanner\scan\main.nf line 48:

    -genome $fasta \
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -genome "$fasta" \

In .\modules\nf-core\helitronscanner\scan\main.nf line 49:

    -buffer_size $buffer_size \
                 ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -buffer_size "$buffer_size" \

In .\modules\nf-core\helitronscanner\scan\main.nf line 50:

    -threads_LCV $task.cpus \
                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -threads_LCV "$task".cpus \

In .\modules\nf-core\helitronscanner\scan\main.nf line 51:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\helitronscanner\scan\main.nf line 52:

    -output ${prefix}.${command}
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -output "${prefix}"."${command}"

For more information:
  https://www.shellcheck.net/wiki/SC1091 -- Not following: /usr/local/env-act...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hhsuite\reformat\main.nf:

In .\modules\nf-core\hhsuite\reformat\main.nf line 32:

    gzip -c -d $aln > $aln_name
               ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "$aln" > "$aln_name"

In .\modules\nf-core\hhsuite\reformat\main.nf line 36:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hhsuite\reformat\main.nf line 37:

    ${informat} \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${informat}" \

In .\modules\nf-core\hhsuite\reformat\main.nf line 38:

    ${outformat} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${outformat}" \

In .\modules\nf-core\hhsuite\reformat\main.nf line 39:

    ${aln_name} \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${aln_name}" \

In .\modules\nf-core\hhsuite\reformat\main.nf line 40:

    ${prefix}.${outformat}
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"."${outformat}"

In .\modules\nf-core\hhsuite\reformat\main.nf line 42:

gzip ${prefix}.${outformat}
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
               ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip "${prefix}"."${outformat}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hicap\main.nf:

In .\modules\nf-core\hicap\main.nf line 33:

    gzip -c -d $fasta > $fasta_name
               ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "$fasta" > "$fasta_name"

In .\modules\nf-core\hicap\main.nf line 36:

    --query_fp $fasta_name \
               ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --query_fp "$fasta_name" \

In .\modules\nf-core\hicap\main.nf line 37:

    $database_args \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$database_args" \

In .\modules\nf-core\hicap\main.nf line 38:

    $model_args \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$model_args" \

In .\modules\nf-core\hicap\main.nf line 39:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hicap\main.nf line 40:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hicexplorer\hicpca\main.nf:

In .\modules\nf-core\hicexplorer\hicpca\main.nf line 44:

    -m $matrix \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -m "$matrix" \

In .\modules\nf-core\hicexplorer\hicpca\main.nf line 45:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hicexplorer\hicpca\main.nf line 46:

    --format $format \
             ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --format "$format" \

In .\modules\nf-core\hicexplorer\hicpca\main.nf line 47:

    --whichEigenvectors $eigenvectors \
                        ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --whichEigenvectors "$eigenvectors" \

In .\modules\nf-core\hicexplorer\hicpca\main.nf line 48:

    --outputFileName ${outfilenames}
                     ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outputFileName "${outfilenames}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hifiasm\main.nf:

In .\modules\nf-core\hifiasm\main.nf line 63:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hifiasm\main.nf line 64:

    -t ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "${task.cpus}" \

In .\modules\nf-core\hifiasm\main.nf line 65:

    ${input_trio} \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_trio}" \

In .\modules\nf-core\hifiasm\main.nf line 66:

    ${input_hic} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_hic}" \

In .\modules\nf-core\hifiasm\main.nf line 67:

    ${ultralong} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${ultralong}" \

In .\modules\nf-core\hifiasm\main.nf line 68:

    -o ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}" \

In .\modules\nf-core\hifiasm\main.nf line 69:

    ${long_reads_sorted} \
    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${long_reads_sorted}" \

In .\modules\nf-core\hifiasm\main.nf line 70:

    2> >( tee ${prefix}.stderr.log >&2 )
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    2> >( tee "${prefix}".stderr.log >&2 )

In .\modules\nf-core\hifiasm\main.nf line 72:

if [ -f ${prefix}.ec.fa ]; then
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
if [ -f "${prefix}".ec.fa ]; then

In .\modules\nf-core\hifiasm\main.nf line 73:

    gzip ${prefix}.ec.fa
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip "${prefix}".ec.fa

In .\modules\nf-core\hifiasm\main.nf line 76:

if [ -f ${prefix}.ovlp.paf ]; then
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
if [ -f "${prefix}".ovlp.paf ]; then

In .\modules\nf-core\hifiasm\main.nf line 77:

    gzip ${prefix}.ovlp.paf
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip "${prefix}".ovlp.paf

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hiphase\main.nf:

In .\modules\nf-core\hiphase\main.nf line 29:

    --bam $bam \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bam "$bam" \

In .\modules\nf-core\hiphase\main.nf line 30:

    --vcf $vcf \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --vcf "$vcf" \

In .\modules\nf-core\hiphase\main.nf line 31:

    --output-vcf ${prefix}.phased.vcf \
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-vcf "${prefix}".phased.vcf \

In .\modules\nf-core\hiphase\main.nf line 32:

    --output-bam ${prefix}.phased.bam \
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-bam "${prefix}".phased.bam \

In .\modules\nf-core\hiphase\main.nf line 33:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\hiphase\main.nf line 34:

    --stats-file ${prefix}.stats.csv \
                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --stats-file "${prefix}".stats.csv \

In .\modules\nf-core\hiphase\main.nf line 35:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hiphase\main.nf line 36:

    --threads ${task.cpus}
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hisat2\align\main.nf:

In .\modules\nf-core\hisat2\align\main.nf line 39:

INDEX=`find -L ./ -name "*.1.ht2" | sed 's/\.1.ht2\$//'`
^---^ SC2034 (warning): INDEX appears unused. Verify use (or export if used externally).
      ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.

Did you mean: 
INDEX=$(find -L ./ -name "*.1.ht2" | sed 's/\.1.ht2\$//')

In .\modules\nf-core\hisat2\align\main.nf line 42:

    -U $reads \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -U "$reads" \

In .\modules\nf-core\hisat2\align\main.nf line 43:

    $strandedness \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$strandedness" \

In .\modules\nf-core\hisat2\align\main.nf line 44:

    $ss \
    ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$ss" \

In .\modules\nf-core\hisat2\align\main.nf line 45:

    --summary-file ${prefix}.hisat2.summary.log \
                   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --summary-file "${prefix}".hisat2.summary.log \

In .\modules\nf-core\hisat2\align\main.nf line 46:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\hisat2\align\main.nf line 47:

    $seq_center \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$seq_center" \

In .\modules\nf-core\hisat2\align\main.nf line 48:

    $unaligned \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$unaligned" \

In .\modules\nf-core\hisat2\align\main.nf line 49:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hisat2\align\main.nf line 50:

    | samtools view -bS -F 4 -F 256 - > ${prefix}.bam
                                        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | samtools view -bS -F 4 -F 256 - > "${prefix}".bam

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- INDEX appears unused. Verify use ...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\hisat2\build\main.nf:

In .\modules\nf-core\hisat2\build\main.nf line 52:

    -p ${task.cpus} \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "${task.cpus}" \

In .\modules\nf-core\hisat2\build\main.nf line 53:

    ${ss} \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${ss}" \

In .\modules\nf-core\hisat2\build\main.nf line 54:

    ${exon} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${exon}" \

In .\modules\nf-core\hisat2\build\main.nf line 55:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\hisat2\build\main.nf line 56:

    ${fasta} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fasta}" \

In .\modules\nf-core\hisat2\build\main.nf line 57:

    hisat2/${fasta.baseName}
           ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    hisat2/"${fasta.baseName}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hisat2\extractsplicesites\main.nf:

In .\modules\nf-core\hisat2\extractsplicesites\main.nf line 23:

hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
                               ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                      ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
hisat2_extract_splice_sites.py "$gtf" > "${gtf.baseName}".splice_sites.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hlala\preparegraph\main.nf:

In .\modules\nf-core\hlala\preparegraph\main.nf line 33:

    --PRG_graph_dir $graph
                    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --PRG_graph_dir "$graph"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hlala\typing\main.nf:

In .\modules\nf-core\hlala\typing\main.nf line 43:

    --BAM $bam \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --BAM "$bam" \

In .\modules\nf-core\hlala\typing\main.nf line 44:

    --customGraphDir ${graph} \
                     ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --customGraphDir "${graph}" \

In .\modules\nf-core\hlala\typing\main.nf line 45:

    --sampleID $prefix \
               ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --sampleID "$prefix" \

In .\modules\nf-core\hlala\typing\main.nf line 47:

    --maxThreads $task.cpus \
                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --maxThreads "$task".cpus \

In .\modules\nf-core\hlala\typing\main.nf line 48:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

In .\modules\nf-core\hlala\typing\main.nf line 51:

mv ${prefix}/ results/
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${prefix}"/ results/

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmcopy\gccounter\main.nf:

In .\modules\nf-core\hmmcopy\gccounter\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmcopy\gccounter\main.nf line 27:

    ${fasta} > ${prefix}.wig
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fasta}" > "${prefix}".wig

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmcopy\generatemap\main.nf:

In .\modules\nf-core\hmmcopy\generatemap\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmcopy\generatemap\main.nf line 29:

    $fasta
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta"

In .\modules\nf-core\hmmcopy\generatemap\main.nf line 33:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmcopy\generatemap\main.nf line 34:

    $fasta
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmcopy\mapcounter\main.nf:

In .\modules\nf-core\hmmcopy\mapcounter\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmcopy\mapcounter\main.nf line 27:

    $bigwig > ${prefix}.wig
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
              ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bigwig" > "${prefix}".wig

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmcopy\readcounter\main.nf:

In .\modules\nf-core\hmmcopy\readcounter\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmcopy\readcounter\main.nf line 28:

    ${bam} > ${prefix}.wig
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bam}" > "${prefix}".wig

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmer\eslalimask\main.nf:

In .\modules\nf-core\hmmer\eslalimask\main.nf line 38:

    $fmask_rfarg \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fmask_rfarg" \

In .\modules\nf-core\hmmer\eslalimask\main.nf line 39:

    $fmask_allarg \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fmask_allarg" \

In .\modules\nf-core\hmmer\eslalimask\main.nf line 40:

    $gmask_rfarg \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gmask_rfarg" \

In .\modules\nf-core\hmmer\eslalimask\main.nf line 41:

    $gmask_allarg \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gmask_allarg" \

In .\modules\nf-core\hmmer\eslalimask\main.nf line 42:

    $pmask_rfarg \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$pmask_rfarg" \

In .\modules\nf-core\hmmer\eslalimask\main.nf line 43:

    $pmask_allarg \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$pmask_allarg" \

In .\modules\nf-core\hmmer\eslalimask\main.nf line 44:

    -o ${prefix}.masked.sthlm \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".masked.sthlm \

In .\modules\nf-core\hmmer\eslalimask\main.nf line 45:

    $args $unmaskedaln $maskfile
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
          ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" "$unmaskedaln" "$maskfile"

In .\modules\nf-core\hmmer\eslalimask\main.nf line 47:

gzip ${prefix}.*mask*
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip "${prefix}".*mask*

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmer\eslreformat\main.nf:

In .\modules\nf-core\hmmer\eslreformat\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmer\eslreformat\main.nf line 29:

    $seqfile \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$seqfile" \

In .\modules\nf-core\hmmer\eslreformat\main.nf line 30:

    $postproc \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$postproc" \

In .\modules\nf-core\hmmer\eslreformat\main.nf line 31:

    | gzip -c > ${prefix}.${suffix}.gz
                ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    | gzip -c > "${prefix}"."${suffix}".gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmer\hmmalign\main.nf:

In .\modules\nf-core\hmmer\hmmalign\main.nf line 26:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmer\hmmalign\main.nf line 27:

    $hmm \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$hmm" \

In .\modules\nf-core\hmmer\hmmalign\main.nf line 28:

    $fasta | gzip -c > ${prefix}.sto.gz
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta" | gzip -c > "${prefix}".sto.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmer\hmmbuild\main.nf:

In .\modules\nf-core\hmmer\hmmbuild\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmer\hmmbuild\main.nf line 30:

    --cpu $task.cpus \
          ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpu "$task".cpus \

In .\modules\nf-core\hmmer\hmmbuild\main.nf line 31:

    -n ${prefix}  \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -n "${prefix}"  \

In .\modules\nf-core\hmmer\hmmbuild\main.nf line 32:

    -o ${prefix}.hmmbuild.txt \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".hmmbuild.txt \

In .\modules\nf-core\hmmer\hmmbuild\main.nf line 33:

    ${mxfileopt} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${mxfileopt}" \

In .\modules\nf-core\hmmer\hmmbuild\main.nf line 34:

    ${prefix}.hmm \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".hmm \

In .\modules\nf-core\hmmer\hmmbuild\main.nf line 35:

    $alignment
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$alignment"

In .\modules\nf-core\hmmer\hmmbuild\main.nf line 37:

gzip ${prefix}.hmm
     ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
gzip "${prefix}".hmm

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmer\hmmfetch\main.nf:

In .\modules\nf-core\hmmer\hmmfetch\main.nf line 37:

    $kfopt \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$kfopt" \

In .\modules\nf-core\hmmer\hmmfetch\main.nf line 38:

    $index \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$index" \

In .\modules\nf-core\hmmer\hmmfetch\main.nf line 39:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmer\hmmfetch\main.nf line 40:

    $hmm \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$hmm" \

In .\modules\nf-core\hmmer\hmmfetch\main.nf line 41:

    $keyarg \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$keyarg" \

In .\modules\nf-core\hmmer\hmmfetch\main.nf line 42:

    $keyfile \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$keyfile" \

In .\modules\nf-core\hmmer\hmmfetch\main.nf line 43:

    $outfile
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$outfile"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmer\hmmpress\main.nf:

In .\modules\nf-core\hmmer\hmmpress\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmer\hmmpress\main.nf line 26:

    ${hmmfile}
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${hmmfile}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmer\hmmrank\main.nf:

In .\modules\nf-core\hmmer\hmmrank\main.nf line 25:

#!/usr/bin/env Rscript
^-- SC1128 (error): The shebang must be on the first line. Delete blanks and move comments.

In .\modules\nf-core\hmmer\hmmrank\main.nf line 26:

library(readr)
^-- SC1073 (error): Couldn't parse this function. Fix to allow more checks.
        ^-- SC1065 (error): Trying to declare parameters? Don't. Use () and refer to params as $1, $2..

In .\modules\nf-core\hmmer\hmmrank\main.nf line 27:

library(dplyr)
^-- SC1064 (error): Expected a { to open the function definition.
^-- SC1072 (error):  Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1064 -- Expected a { to open the function...
  https://www.shellcheck.net/wiki/SC1065 -- Trying to declare parameters? Don...
  https://www.shellcheck.net/wiki/SC1128 -- The shebang must be on the first ...

ShellCheck results for .\modules\nf-core\hmmer\hmmsearch\main.nf:

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 32:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 33:

    --cpu $task.cpus \
          ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpu "$task".cpus \

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 34:

    -o $output \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "$output" \

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 35:

    $alignment \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$alignment" \

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 36:

    $target_summary \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$target_summary" \

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 37:

    $domain_summary \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$domain_summary" \

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 38:

    $hmmfile \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$hmmfile" \

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 39:

    $seqdb
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$seqdb"

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 41:

gzip --no-name *.txt \
               ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 42:

    ${write_align ? '*.sto' : ''} \
    ^---------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${write_align ? '*.sto' : ''}" \

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 43:

    ${write_target ? '*.tbl' : ''} \
    ^----------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${write_target ? '*.tbl' : ''}" \

In .\modules\nf-core\hmmer\hmmsearch\main.nf line 44:

    ${write_domain ? '*.domtbl' : ''}
    ^-- SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${write_domain ? '*.domtbl' : ''}"

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmmer\jackhmmer\main.nf:

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 31:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 32:

    --cpu $task.cpus \
          ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpu "$task".cpus \

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 33:

    -o ${prefix}.txt \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".txt \

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 34:

    $alignment \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$alignment" \

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 35:

    $target_summary \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$target_summary" \

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 36:

    $domain_summary \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$domain_summary" \

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 37:

    ${fasta} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fasta}" \

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 38:

    ${seqdb}
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${seqdb}"

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 40:

gzip --no-name *.txt \
               ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 41:

    ${write_align ? '*.sto' : ''} \
    ^---------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${write_align ? '*.sto' : ''}" \

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 42:

    ${write_target ? '*.tbl' : ''} \
    ^----------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${write_target ? '*.tbl' : ''}" \

In .\modules\nf-core\hmmer\jackhmmer\main.nf line 43:

    ${write_domain ? '*.domtbl' : ''}
    ^-- SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${write_domain ? '*.domtbl' : ''}"

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hmtnote\annotate\main.nf:

In .\modules\nf-core\hmtnote\annotate\main.nf line 27:

    $vcf \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf" \

In .\modules\nf-core\hmtnote\annotate\main.nf line 28:

    ${prefix}_annotated.vcf \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"_annotated.vcf \

In .\modules\nf-core\hmtnote\annotate\main.nf line 29:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\homer\annotatepeaks\main.nf:

In .\modules\nf-core\homer\annotatepeaks\main.nf line 29:

    ${peak} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${peak}" \

In .\modules\nf-core\homer\annotatepeaks\main.nf line 30:

    ${fasta} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fasta}" \

In .\modules\nf-core\homer\annotatepeaks\main.nf line 31:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\homer\annotatepeaks\main.nf line 32:

    -gtf ${gtf} \
         ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -gtf "${gtf}" \

In .\modules\nf-core\homer\annotatepeaks\main.nf line 33:

    -cpu ${task.cpus} \
         ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -cpu "${task.cpus}" \

In .\modules\nf-core\homer\annotatepeaks\main.nf line 34:

    > ${prefix}.annotatePeaks.txt
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".annotatePeaks.txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\homer\findpeaks\main.nf:

In .\modules\nf-core\homer\findpeaks\main.nf line 29:

    ${tagDir} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${tagDir}" \

In .\modules\nf-core\homer\findpeaks\main.nf line 30:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\homer\findpeaks\main.nf line 31:

    -o ${prefix}.peaks.txt \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".peaks.txt \

In .\modules\nf-core\homer\findpeaks\main.nf line 32:

    ${uniqmap_flag}
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${uniqmap_flag}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\homer\maketagdirectory\main.nf:

In .\modules\nf-core\homer\maketagdirectory\main.nf line 28:

    ${prefix}_tagdir \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}"_tagdir \

In .\modules\nf-core\homer\maketagdirectory\main.nf line 29:

    -genome ${fasta} \
            ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -genome "${fasta}" \

In .\modules\nf-core\homer\maketagdirectory\main.nf line 30:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\homer\maketagdirectory\main.nf line 31:

    ${bam}
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bam}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\homer\makeucscfile\main.nf:

In .\modules\nf-core\homer\makeucscfile\main.nf line 26:

    ${tagDir} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${tagDir}" \

In .\modules\nf-core\homer\makeucscfile\main.nf line 27:

    -o ${prefix}.bedGraph \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".bedGraph \

In .\modules\nf-core\homer\makeucscfile\main.nf line 28:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\homer\pos2bed\main.nf:

In .\modules\nf-core\homer\pos2bed\main.nf line 25:

pos2bed.pl ${peaks} > ${prefix}.bed
           ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
pos2bed.pl "${peaks}" > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hostile\clean\main.nf:

In .\modules\nf-core\hostile\clean\main.nf line 35:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\hostile\clean\main.nf line 36:

    --threads ${task.cpus} \
              ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "${task.cpus}" \

In .\modules\nf-core\hostile\clean\main.nf line 37:

    ${reads_cmd} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${reads_cmd}" \

In .\modules\nf-core\hostile\clean\main.nf line 38:

    --index ${reference_dir}/${reference_name} \
            ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                             ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --index "${reference_dir}"/"${reference_name}" \

In .\modules\nf-core\hostile\clean\main.nf line 42:

    |tee > ${prefix}.json
           ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    |tee > "${prefix}".json

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hostile\fetch\main.nf:

In .\modules\nf-core\hostile\fetch\main.nf line 24:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hpsuissero\main.nf:

In .\modules\nf-core\hpsuissero\main.nf line 29:

    gzip -c -d $fasta > $fasta_name
               ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "$fasta" > "$fasta_name"

In .\modules\nf-core\hpsuissero\main.nf line 33:

    -i $fasta_name \
       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$fasta_name" \

In .\modules\nf-core\hpsuissero\main.nf line 35:

    -s $prefix \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -s "$prefix" \

In .\modules\nf-core\hpsuissero\main.nf line 37:

    -t $task.cpus
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\htseq\count\main.nf:

In .\modules\nf-core\htseq\count\main.nf line 27:

    ${input} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input}" \

In .\modules\nf-core\htseq\count\main.nf line 28:

    ${gtf} \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${gtf}" \

In .\modules\nf-core\htseq\count\main.nf line 29:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\htseq\count\main.nf line 30:

    > ${prefix}.txt
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\htsnimtools\vcfcheck\main.nf:

In .\modules\nf-core\htsnimtools\vcfcheck\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\htsnimtools\vcfcheck\main.nf line 28:

    $background_vcf \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$background_vcf" \

In .\modules\nf-core\htsnimtools\vcfcheck\main.nf line 29:

    $vcf \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$vcf" \

In .\modules\nf-core\htsnimtools\vcfcheck\main.nf line 30:

    > ${prefix}.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\humid\main.nf:

In .\modules\nf-core\humid\main.nf line 33:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\humid\main.nf line 34:

    -d ${prefix} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -d "${prefix}" \

In .\modules\nf-core\humid\main.nf line 35:

    -l ${prefix}.log \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -l "${prefix}".log \

In .\modules\nf-core\humid\main.nf line 36:

    $reads \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reads" \

In .\modules\nf-core\humid\main.nf line 37:

    $umis \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$umis" \

In .\modules\nf-core\humid\main.nf line 39:

mv ${prefix}/*.fastq* .
   ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "${prefix}"/*.fastq* .

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\hypo\main.nf:

In .\modules\nf-core\hypo\main.nf line 32:

    -d $draft \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -d "$draft" \

In .\modules\nf-core\hypo\main.nf line 33:

    -b $sr_bam \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "$sr_bam" \

In .\modules\nf-core\hypo\main.nf line 34:

    -c $reads_coverage \
       ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -c "$reads_coverage" \

In .\modules\nf-core\hypo\main.nf line 35:

    -s $genome_size \
       ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -s "$genome_size" \

In .\modules\nf-core\hypo\main.nf line 36:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\hypo\main.nf line 37:

    -o ${prefix}.fasta \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".fasta \

In .\modules\nf-core\hypo\main.nf line 38:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ichorcna\createpon\main.nf:

In .\modules\nf-core\ichorcna\createpon\main.nf line 34:

#!/usr/bin/env Rscript
^-- SC1128 (error): The shebang must be on the first line. Delete blanks and move comments.

In .\modules\nf-core\ichorcna\createpon\main.nf line 35:

library("ichorCNA")
^-- SC1073 (error): Couldn't parse this function. Fix to allow more checks.
        ^-- SC1065 (error): Trying to declare parameters? Don't. Use () and refer to params as $1, $2..

In .\modules\nf-core\ichorcna\createpon\main.nf line 36:

library("yaml")
^-- SC1064 (error): Expected a { to open the function definition.
^-- SC1072 (error):  Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1064 -- Expected a { to open the function...
  https://www.shellcheck.net/wiki/SC1065 -- Trying to declare parameters? Don...
  https://www.shellcheck.net/wiki/SC1128 -- The shebang must be on the first ...

ShellCheck results for .\modules\nf-core\ichorcna\run\main.nf:

In .\modules\nf-core\ichorcna\run\main.nf line 44:

#!/usr/bin/env Rscript
^-- SC1128 (error): The shebang must be on the first line. Delete blanks and move comments.

In .\modules\nf-core\ichorcna\run\main.nf line 45:

library("ichorCNA")
^-- SC1073 (error): Couldn't parse this function. Fix to allow more checks.
        ^-- SC1065 (error): Trying to declare parameters? Don't. Use () and refer to params as $1, $2..

In .\modules\nf-core\ichorcna\run\main.nf line 46:

library("yaml")
^-- SC1064 (error): Expected a { to open the function definition.
^-- SC1072 (error):  Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1064 -- Expected a { to open the function...
  https://www.shellcheck.net/wiki/SC1065 -- Trying to declare parameters? Don...
  https://www.shellcheck.net/wiki/SC1128 -- The shebang must be on the first ...

ShellCheck results for .\modules\nf-core\icountmini\metagene\main.nf:

In .\modules\nf-core\icountmini\metagene\main.nf line 26:

mv $bed ${prefix}.bed
   ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv "$bed" "${prefix}".bed

In .\modules\nf-core\icountmini\metagene\main.nf line 29:

    ${prefix}.bed \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".bed \

In .\modules\nf-core\icountmini\metagene\main.nf line 30:

    $segmentation \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$segmentation" \

In .\modules\nf-core\icountmini\metagene\main.nf line 31:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\icountmini\peaks\main.nf:

In .\modules\nf-core\icountmini\peaks\main.nf line 25:

    $bed \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bed" \

In .\modules\nf-core\icountmini\peaks\main.nf line 26:

    $sigxls \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sigxls" \

In .\modules\nf-core\icountmini\peaks\main.nf line 27:

    ${prefix}.peaks.bed.gz \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".peaks.bed.gz \

In .\modules\nf-core\icountmini\peaks\main.nf line 28:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\icountmini\segment\main.nf:

In .\modules\nf-core\icountmini\segment\main.nf line 28:

    $gtf \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$gtf" \

In .\modules\nf-core\icountmini\segment\main.nf line 29:

    ${prefix}.gtf \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".gtf \

In .\modules\nf-core\icountmini\segment\main.nf line 30:

    $fai
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fai"

In .\modules\nf-core\icountmini\segment\main.nf line 32:

mv regions.gtf.gz ${regions_prefix}_regions.gtf.gz
                  ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv regions.gtf.gz "${regions_prefix}"_regions.gtf.gz

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\icountmini\sigxls\main.nf:

In .\modules\nf-core\icountmini\sigxls\main.nf line 27:

    $segmentation \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$segmentation" \

In .\modules\nf-core\icountmini\sigxls\main.nf line 28:

    $bed \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bed" \

In .\modules\nf-core\icountmini\sigxls\main.nf line 29:

    ${prefix}.sigxls.bed.gz \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".sigxls.bed.gz \

In .\modules\nf-core\icountmini\sigxls\main.nf line 30:

    --scores ${prefix}.scores.tsv \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --scores "${prefix}".scores.tsv \

In .\modules\nf-core\icountmini\sigxls\main.nf line 31:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\icountmini\summary\main.nf:

In .\modules\nf-core\icountmini\summary\main.nf line 28:

    $segmentation \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$segmentation" \

In .\modules\nf-core\icountmini\summary\main.nf line 29:

    $bed \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bed" \

In .\modules\nf-core\icountmini\summary\main.nf line 31:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

In .\modules\nf-core\icountmini\summary\main.nf line 33:

mv summary_type.tsv ${prefix}.summary_type.tsv
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv summary_type.tsv "${prefix}".summary_type.tsv

In .\modules\nf-core\icountmini\summary\main.nf line 34:

mv summary_subtype.tsv ${prefix}.summary_subtype.tsv
                       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv summary_subtype.tsv "${prefix}".summary_subtype.tsv

In .\modules\nf-core\icountmini\summary\main.nf line 35:

mv summary_gene.tsv ${prefix}.summary_gene.tsv
                    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mv summary_gene.tsv "${prefix}".summary_gene.tsv

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\idemux\main.nf:

In .\modules\nf-core\idemux\main.nf line 27:

    --r1 ${reads[0]} \
         ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --r1 "${reads[0]}" \

In .\modules\nf-core\idemux\main.nf line 28:

    --r2 ${reads[1]} \
         ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --r2 "${reads[1]}" \

In .\modules\nf-core\idemux\main.nf line 29:

    --sample-sheet ${samplesheet} \
                   ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --sample-sheet "${samplesheet}" \

In .\modules\nf-core\idemux\main.nf line 31:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\idr\main.nf:

In .\modules\nf-core\idr\main.nf line 37:

    --samples $peaks \
              ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --samples "$peaks" \

In .\modules\nf-core\idr\main.nf line 38:

    --input-file-type $peak_type \
                      ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --input-file-type "$peak_type" \

In .\modules\nf-core\idr\main.nf line 39:

    --output-file $idr_vals \
                  ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output-file "$idr_vals" \

In .\modules\nf-core\idr\main.nf line 40:

    --log-output-file $log_file \
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --log-output-file "$log_file" \

In .\modules\nf-core\idr\main.nf line 42:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\igv\js\main.nf:

In .\modules\nf-core\igv\js\main.nf line 27:

cat  <<IGV > ${prefix}_genome-browser.html
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
cat  <<IGV > "${prefix}"_genome-browser.html

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\igvreports\main.nf:

In .\modules\nf-core\igvreports\main.nf line 35:

create_report $sites \
              ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
create_report "$sites" \

In .\modules\nf-core\igvreports\main.nf line 36:

$args \
^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
"$args" \

In .\modules\nf-core\igvreports\main.nf line 37:

$fasta \
^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
"$fasta" \

In .\modules\nf-core\igvreports\main.nf line 38:

$track_arg \
^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
"$track_arg" \

In .\modules\nf-core\igvreports\main.nf line 39:

--output ${prefix}_report.html
         ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
--output "${prefix}"_report.html

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ilastik\multicut\main.nf:

In .\modules\nf-core\ilastik\multicut\main.nf line 33:

    --project=$ilp \
              ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --project="$ilp" \

In .\modules\nf-core\ilastik\multicut\main.nf line 34:

    --raw_data=$h5 \
               ^-^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --raw_data="$h5" \

In .\modules\nf-core\ilastik\multicut\main.nf line 35:

    --probabilities=${probs} \
                    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --probabilities="${probs}" \

In .\modules\nf-core\ilastik\multicut\main.nf line 37:

    --output_filename_format=${prefix}.tiff \
                             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output_filename_format="${prefix}".tiff \

In .\modules\nf-core\ilastik\multicut\main.nf line 38:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ilastik\pixelclassification\main.nf:

In .\modules\nf-core\ilastik\pixelclassification\main.nf line 32:

    --project=${ilp} \
              ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --project="${ilp}" \

In .\modules\nf-core\ilastik\pixelclassification\main.nf line 33:

    --output_filename_format=${prefix}.${output_format} \
                             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                       ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --output_filename_format="${prefix}"."${output_format}" \

In .\modules\nf-core\ilastik\pixelclassification\main.nf line 34:

    --export_source=${export_source} \
                    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --export_source="${export_source}" \

In .\modules\nf-core\ilastik\pixelclassification\main.nf line 35:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\ilastik\pixelclassification\main.nf line 36:

    ${input_img}
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${input_img}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\immunedeconv\main.nf:

In .\modules\nf-core\immunedeconv\main.nf line 28:

touch ${prefix}.deconvolution_results.tsv
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".deconvolution_results.tsv

In .\modules\nf-core\immunedeconv\main.nf line 29:

touch ${prefix}.plot1_stacked_bar_chart.png
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".plot1_stacked_bar_chart.png

In .\modules\nf-core\immunedeconv\main.nf line 30:

touch ${prefix}.plot2_points_with_facets.png
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
touch "${prefix}".plot2_points_with_facets.png

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\infernal\cmsearch\main.nf:

In .\modules\nf-core\infernal\cmsearch\main.nf line 37:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\infernal\cmsearch\main.nf line 38:

    --cpu ${task.cpus} \
          ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpu "${task.cpus}" \

In .\modules\nf-core\infernal\cmsearch\main.nf line 39:

    -o ${output} \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${output}" \

In .\modules\nf-core\infernal\cmsearch\main.nf line 40:

    ${alignment} \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${alignment}" \

In .\modules\nf-core\infernal\cmsearch\main.nf line 41:

    ${target_summary} \
    ^---------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${target_summary}" \

In .\modules\nf-core\infernal\cmsearch\main.nf line 42:

    ${cmfile} \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${cmfile}" \

In .\modules\nf-core\infernal\cmsearch\main.nf line 43:

    ${seqdb_input}
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${seqdb_input}"

In .\modules\nf-core\infernal\cmsearch\main.nf line 45:

gzip --no-name *.txt \
               ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.

In .\modules\nf-core\infernal\cmsearch\main.nf line 46:

    ${write_align ? '*.sto' : ''} \
    ^---------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${write_align ? '*.sto' : ''}" \

In .\modules\nf-core\infernal\cmsearch\main.nf line 47:

    ${write_target ? '*.tbl' : ''}
    ^----------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${write_target ? '*.tbl' : ''}"

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\instrain\compare\main.nf:

In .\modules\nf-core\instrain\compare\main.nf line 32:

    -i $profiles \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$profiles" \

In .\modules\nf-core\instrain\compare\main.nf line 33:

    -o ${prefix}.IS_compare \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".IS_compare \

In .\modules\nf-core\instrain\compare\main.nf line 34:

    --processes $task.cpus \
                ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --processes "$task".cpus \

In .\modules\nf-core\instrain\compare\main.nf line 35:

    --bams $bams \
           ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bams "$bams" \

In .\modules\nf-core\instrain\compare\main.nf line 36:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\instrain\profile\main.nf:

In .\modules\nf-core\instrain\profile\main.nf line 37:

    $bam \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam" \

In .\modules\nf-core\instrain\profile\main.nf line 38:

    $genome_fasta \
    ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$genome_fasta" \

In .\modules\nf-core\instrain\profile\main.nf line 39:

    -o ${prefix}.IS \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".IS \

In .\modules\nf-core\instrain\profile\main.nf line 40:

    -p $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "$task".cpus \

In .\modules\nf-core\instrain\profile\main.nf line 41:

    $genes_args \
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$genes_args" \

In .\modules\nf-core\instrain\profile\main.nf line 42:

    $stb_args \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$stb_args" \

In .\modules\nf-core\instrain\profile\main.nf line 43:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\integronfinder\main.nf:

In .\modules\nf-core\integronfinder\main.nf line 34:

    gzip -c -d $fasta > $fasta_name
               ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                        ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    gzip -c -d "$fasta" > "$fasta_name"

In .\modules\nf-core\integronfinder\main.nf line 38:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\integronfinder\main.nf line 39:

    --cpu $task.cpus \
          ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --cpu "$task".cpus \

In .\modules\nf-core\integronfinder\main.nf line 40:

    $fasta_name
    ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$fasta_name"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\interproscan\main.nf:

In .\modules\nf-core\interproscan\main.nf line 31:

if [ -d 'data' ]; then
^-- SC1046 (error): Couldn't find 'fi' for this 'if'.
^-- SC1073 (error): Couldn't parse this if expression. Fix to allow more checks.

In .\modules\nf-core\interproscan\main.nf line 33:

    INTERPROSCAN_DIR="\$( dirname "\$( dirname "\$( which interproscan.sh )" )" )"
                                     ^-- SC1036 (error): '(' is invalid here. Did you forget to escape it?
                                     ^-- SC1047 (error): Expected 'fi' matching previously mentioned 'if'.
                                     ^-- SC1072 (error): Expected 'fi'. Fix any mentioned problems and try again.

For more information:
  https://www.shellcheck.net/wiki/SC1046 -- Couldn't find 'fi' for this 'if'.
  https://www.shellcheck.net/wiki/SC1036 -- '(' is invalid here. Did you forg...
  https://www.shellcheck.net/wiki/SC1047 -- Expected 'fi' matching previously...

ShellCheck results for .\modules\nf-core\iphop\download\main.nf:

In .\modules\nf-core\iphop\download\main.nf line 26:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

In .\modules\nf-core\iphop\download\main.nf line 36:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\iphop\predict\main.nf:

In .\modules\nf-core\iphop\predict\main.nf line 30:

    --fa_file $fasta \
              ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --fa_file "$fasta" \

In .\modules\nf-core\iphop\predict\main.nf line 32:

    --db_dir $iphop_db \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --db_dir "$iphop_db" \

In .\modules\nf-core\iphop\predict\main.nf line 33:

    --num_threads $task.cpus \
                  ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --num_threads "$task".cpus \

In .\modules\nf-core\iphop\predict\main.nf line 34:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\iqtree\main.nf:

In .\modules\nf-core\iqtree\main.nf line 73:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\iqtree\main.nf line 74:

    $alignment_arg \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$alignment_arg" \

In .\modules\nf-core\iqtree\main.nf line 75:

    $tree_arg \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$tree_arg" \

In .\modules\nf-core\iqtree\main.nf line 76:

    $tree_te_arg \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$tree_te_arg" \

In .\modules\nf-core\iqtree\main.nf line 77:

    $lmclust_arg \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$lmclust_arg" \

In .\modules\nf-core\iqtree\main.nf line 78:

    $mdef_arg \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$mdef_arg" \

In .\modules\nf-core\iqtree\main.nf line 79:

    $partitions_equal_arg \
    ^-------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$partitions_equal_arg" \

In .\modules\nf-core\iqtree\main.nf line 80:

    $partitions_proportional_arg \
    ^--------------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$partitions_proportional_arg" \

In .\modules\nf-core\iqtree\main.nf line 81:

    $partitions_unlinked_arg \
    ^----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$partitions_unlinked_arg" \

In .\modules\nf-core\iqtree\main.nf line 82:

    $guide_tree_arg \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$guide_tree_arg" \

In .\modules\nf-core\iqtree\main.nf line 83:

    $sitefreq_in_arg \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$sitefreq_in_arg" \

In .\modules\nf-core\iqtree\main.nf line 84:

    $constraint_tree_arg \
    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$constraint_tree_arg" \

In .\modules\nf-core\iqtree\main.nf line 85:

    $trees_z_arg \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$trees_z_arg" \

In .\modules\nf-core\iqtree\main.nf line 86:

    $suptree_arg \
    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$suptree_arg" \

In .\modules\nf-core\iqtree\main.nf line 87:

    $trees_rf\
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$trees_rf"\

In .\modules\nf-core\iqtree\main.nf line 88:

    -pre $prefix \
         ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -pre "$prefix" \

In .\modules\nf-core\iqtree\main.nf line 90:

    -ntmax $task.cpus \
           ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -ntmax "$task".cpus \

In .\modules\nf-core\iqtree\main.nf line 91:

    -mem $memory \
         ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -mem "$memory" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\irescue\main.nf:

In .\modules\nf-core\irescue\main.nf line 31:

mkdir -p $prefix
         ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
mkdir -p "$prefix"

In .\modules\nf-core\irescue\main.nf line 34:

    --bam $bam \
          ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --bam "$bam" \

In .\modules\nf-core\irescue\main.nf line 35:

    $reference \
    ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$reference" \

In .\modules\nf-core\irescue\main.nf line 36:

    $genome_assembly \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$genome_assembly" \

In .\modules\nf-core\irescue\main.nf line 37:

    --outdir $prefix \
             ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --outdir "$prefix" \

In .\modules\nf-core\irescue\main.nf line 38:

    --threads $task.cpus \
              ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --threads "$task".cpus \

In .\modules\nf-core\irescue\main.nf line 39:

    $args 2> >(tee -a ${prefix}/irescue.log >&2)
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
                      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" 2> >(tee -a "${prefix}"/irescue.log >&2)

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\islandpath\main.nf:

In .\modules\nf-core\islandpath\main.nf line 28:

    $genome \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$genome" \

In .\modules\nf-core\islandpath\main.nf line 29:

    ${prefix}.gff \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".gff \

In .\modules\nf-core\islandpath\main.nf line 30:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ismapper\main.nf:

In .\modules\nf-core\ismapper\main.nf line 25:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ismapper\main.nf line 26:

    --t $task.cpus \
        ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --t "$task".cpus \

In .\modules\nf-core\ismapper\main.nf line 28:

    --queries $query \
              ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --queries "$query" \

In .\modules\nf-core\ismapper\main.nf line 29:

    --reference $reference \
                ^--------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$reference" \

In .\modules\nf-core\ismapper\main.nf line 30:

    --reads $reads
            ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reads "$reads"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\isoseq\cluster\main.nf:

In .\modules\nf-core\isoseq\cluster\main.nf line 36:

    $bam \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam" \

In .\modules\nf-core\isoseq\cluster\main.nf line 37:

    ${prefix}.transcripts.bam \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".transcripts.bam \

In .\modules\nf-core\isoseq\cluster\main.nf line 38:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\isoseq\refine\main.nf:

In .\modules\nf-core\isoseq\refine\main.nf line 31:

    -j $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -j "$task".cpus \

In .\modules\nf-core\isoseq\refine\main.nf line 32:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\isoseq\refine\main.nf line 33:

    $bam \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam" \

In .\modules\nf-core\isoseq\refine\main.nf line 34:

    $primers \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$primers" \

In .\modules\nf-core\isoseq\refine\main.nf line 35:

    ${prefix}.bam
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".bam

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\isoseq3\tag\main.nf:

In .\modules\nf-core\isoseq3\tag\main.nf line 30:

    -j $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -j "$task".cpus \

In .\modules\nf-core\isoseq3\tag\main.nf line 31:

    --design $design \
             ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --design "$design" \

In .\modules\nf-core\isoseq3\tag\main.nf line 32:

    ${prefix}.5p--3p.bam \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".5p--3p.bam \

In .\modules\nf-core\isoseq3\tag\main.nf line 33:

    ${prefix}.flt.bam \
    ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${prefix}".flt.bam \

In .\modules\nf-core\isoseq3\tag\main.nf line 34:

    $args
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ivar\consensus\main.nf:

In .\modules\nf-core\ivar\consensus\main.nf line 32:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\ivar\consensus\main.nf line 33:

    $args2 \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2" \

In .\modules\nf-core\ivar\consensus\main.nf line 34:

    $bam \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam" \

In .\modules\nf-core\ivar\consensus\main.nf line 35:

    $mpileup \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$mpileup" \

In .\modules\nf-core\ivar\consensus\main.nf line 38:

        $args \
        ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "$args" \

In .\modules\nf-core\ivar\consensus\main.nf line 39:

        -p $prefix
           ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        -p "$prefix"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ivar\trim\main.nf:

In .\modules\nf-core\ivar\trim\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\ivar\trim\main.nf line 28:

    -i $bam \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "$bam" \

In .\modules\nf-core\ivar\trim\main.nf line 29:

    -b $bed \
       ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -b "$bed" \

In .\modules\nf-core\ivar\trim\main.nf line 30:

    -p $prefix \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -p "$prefix" \

In .\modules\nf-core\ivar\trim\main.nf line 31:

    > ${prefix}.ivar.log
      ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    > "${prefix}".ivar.log

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\ivar\variants\main.nf:

In .\modules\nf-core\ivar\variants\main.nf line 34:

    $args2 \
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args2" \

In .\modules\nf-core\ivar\variants\main.nf line 35:

    --reference $fasta \
                ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    --reference "$fasta" \

In .\modules\nf-core\ivar\variants\main.nf line 36:

    $bam \
    ^--^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$bam" \

In .\modules\nf-core\ivar\variants\main.nf line 37:

    $mpileup \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$mpileup" \

In .\modules\nf-core\ivar\variants\main.nf line 40:

        $args \
        ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "$args" \

In .\modules\nf-core\ivar\variants\main.nf line 41:

        $features \
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "$features" \

In .\modules\nf-core\ivar\variants\main.nf line 42:

        -r $fasta \
           ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        -r "$fasta" \

In .\modules\nf-core\ivar\variants\main.nf line 43:

        -p $prefix
           ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        -p "$prefix"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\jasminesv\main.nf:

In .\modules\nf-core\jasminesv\main.nf line 45:

ls *.vcf > vcfs.txt
   ^-- SC2035 (info): Use ./*glob* or -- *glob* so names with dashes won't become options.

In .\modules\nf-core\jasminesv\main.nf line 50:

    out_file=${prefix}.vcf \
             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    out_file="${prefix}".vcf \

In .\modules\nf-core\jasminesv\main.nf line 51:

    threads=${task.cpus} \
            ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    threads="${task.cpus}" \

In .\modules\nf-core\jasminesv\main.nf line 52:

    genome_file=${fasta} \
                ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    genome_file="${fasta}" \

In .\modules\nf-core\jasminesv\main.nf line 53:

    ${bam_argument} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bam_argument}" \

In .\modules\nf-core\jasminesv\main.nf line 54:

    ${iris_argument} \
    ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${iris_argument}" \

In .\modules\nf-core\jasminesv\main.nf line 55:

    ${sample_dists_argument} \
    ^----------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${sample_dists_argument}" \

In .\modules\nf-core\jasminesv\main.nf line 56:

    ${chr_norm_argument} \
    ^------------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${chr_norm_argument}" \

In .\modules\nf-core\jasminesv\main.nf line 57:

    ${args}
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}"

In .\modules\nf-core\jasminesv\main.nf line 59:

if [ -s ${prefix}.vcf ]; then
        ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
if [ -s "${prefix}".vcf ]; then

In .\modules\nf-core\jasminesv\main.nf line 61:

    bgzip --threads ${task.cpus} ${args3} ${prefix}.vcf
                    ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                 ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    bgzip --threads "${task.cpus}" "${args3}" "${prefix}".vcf

In .\modules\nf-core\jasminesv\main.nf line 64:

    cat ${first_vcf} | grep "#" | bgzip --threads ${task.cpus} ${args3} > ${prefix}.vcf.gz
        ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                  ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                               ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                          ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    cat "${first_vcf}" | grep "#" | bgzip --threads "${task.cpus}" "${args3}" > "${prefix}".vcf.gz

For more information:
  https://www.shellcheck.net/wiki/SC2035 -- Use ./*glob* or -- *glob* so name...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\jellyfish\count\main.nf:

In .\modules\nf-core\jellyfish\count\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\jellyfish\count\main.nf line 29:

    -m ${kmer_length} \
       ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -m "${kmer_length}" \

In .\modules\nf-core\jellyfish\count\main.nf line 30:

    -s ${size} \
       ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -s "${size}" \

In .\modules\nf-core\jellyfish\count\main.nf line 31:

    -t $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -t "$task".cpus \

In .\modules\nf-core\jellyfish\count\main.nf line 32:

    -o ${prefix}.jf \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".jf \

In .\modules\nf-core\jellyfish\count\main.nf line 33:

    ${fasta}
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${fasta}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\jellyfish\dump\main.nf:

In .\modules\nf-core\jellyfish\dump\main.nf line 27:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\jellyfish\dump\main.nf line 28:

    ${jf} > ${prefix}.${extension}
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.
            ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                      ^----------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${jf}" > "${prefix}"."${extension}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\jupyternotebook\main.nf:

In .\modules\nf-core\jupyternotebook\main.nf line 75:

jupytext --to notebook --output - --set-kernel ${kernel} ${notebook} > ${notebook}.ipynb
                                               ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                         ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                       ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
jupytext --to notebook --output - --set-kernel "${kernel}" "${notebook}" > "${notebook}".ipynb

In .\modules\nf-core\jupyternotebook\main.nf line 76:

${render_cmd} ${notebook}.ipynb ${notebook}.executed.ipynb
              ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
${render_cmd} "${notebook}".ipynb "${notebook}".executed.ipynb

In .\modules\nf-core\jupyternotebook\main.nf line 77:

jupyter nbconvert --stdin --to html --output ${prefix}.html < ${notebook}.executed.ipynb
                                             ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                              ^---------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
jupyter nbconvert --stdin --to html --output "${prefix}".html < "${notebook}".executed.ipynb

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\jvarkit\dict2bed\main.nf:

In .\modules\nf-core\jvarkit\dict2bed\main.nf line 27:

jvarkit -Xmx${task.memory.giga}g -XX:-UsePerfData -Djava.io.tmpdir=TMP dict2bed ${args} ${dict_files} ${args2} > ${prefix}.bed
            ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                        ^-----------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                                      ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                                                 ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
jvarkit -Xmx"${task.memory.giga}"g -XX:-UsePerfData -Djava.io.tmpdir=TMP dict2bed "${args}" "${dict_files}" "${args2}" > "${prefix}".bed

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\jvarkit\sam2tsv\main.nf:

In .\modules\nf-core\jvarkit\sam2tsv\main.nf line 32:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\jvarkit\sam2tsv\main.nf line 33:

    ${regions_file} \
    ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions_file}" \

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\jvarkit\vcf2table\main.nf:

In .\modules\nf-core\jvarkit\vcf2table\main.nf line 32:

bcftools view ${regions_file} -O v ${args1} "${vcf}" |\
              ^-------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                   ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
bcftools view "${regions_file}" -O v "${args1}" "${vcf}" |\

In .\modules\nf-core\jvarkit\vcf2table\main.nf line 33:

    jvarkit -Xmx${task.memory.giga}g  -XX:-UsePerfData -Djava.io.tmpdir=TMP vcf2table ${ped}  ${args2} > "${prefix}.${extension}"
                ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                      ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.
                                                                                              ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    jvarkit -Xmx"${task.memory.giga}"g  -XX:-UsePerfData -Djava.io.tmpdir=TMP vcf2table "${ped}"  "${args2}" > "${prefix}.${extension}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\jvarkit\vcffilterjdk\main.nf:

In .\modules\nf-core\jvarkit\vcffilterjdk\main.nf line 44:

    ${regions_cmd} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions_cmd}" \

In .\modules\nf-core\jvarkit\vcffilterjdk\main.nf line 45:

    ${args1} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args1}" \

In .\modules\nf-core\jvarkit\vcffilterjdk\main.nf line 47:

    jvarkit -Xmx${task.memory.giga}g -XX:-UsePerfData -Djava.io.tmpdir=TMP vcffilterjdk \
                ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    jvarkit -Xmx"${task.memory.giga}"g -XX:-UsePerfData -Djava.io.tmpdir=TMP vcffilterjdk \

In .\modules\nf-core\jvarkit\vcffilterjdk\main.nf line 48:

        ${pedigree_file} \
        ^--------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "${pedigree_file}" \

In .\modules\nf-core\jvarkit\vcffilterjdk\main.nf line 49:

        ${script_file} \
        ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "${script_file}" \

In .\modules\nf-core\jvarkit\vcffilterjdk\main.nf line 50:

        ${args2} |\
        ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "${args2}" |\

In .\modules\nf-core\jvarkit\vcffilterjdk\main.nf line 53:

        ${args3}
        ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "${args3}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\jvarkit\vcfpolyx\main.nf:

In .\modules\nf-core\jvarkit\vcfpolyx\main.nf line 39:

    ${regions_cmd} \
    ^------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${regions_cmd}" \

In .\modules\nf-core\jvarkit\vcfpolyx\main.nf line 40:

    ${args1} \
    ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args1}" \

In .\modules\nf-core\jvarkit\vcfpolyx\main.nf line 42:

    jvarkit -Xmx${task.memory.giga}g  -XX:-UsePerfData -Djava.io.tmpdir=TMP vcfpolyx \
                ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    jvarkit -Xmx"${task.memory.giga}"g  -XX:-UsePerfData -Djava.io.tmpdir=TMP vcfpolyx \

In .\modules\nf-core\jvarkit\vcfpolyx\main.nf line 44:

        ${args2} |\
        ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "${args2}" |\

In .\modules\nf-core\jvarkit\vcfpolyx\main.nf line 47:

        ${args3}
        ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
        "${args3}"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\jvarkit\wgscoverageplotter\main.nf:

In .\modules\nf-core\jvarkit\wgscoverageplotter\main.nf line 28:

jvarkit -Xmx${task.memory.giga}g  -XX:-UsePerfData -Djava.io.tmpdir=TMP wgscoverageplotter \
            ^-----------------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
jvarkit -Xmx"${task.memory.giga}"g  -XX:-UsePerfData -Djava.io.tmpdir=TMP wgscoverageplotter \

In .\modules\nf-core\jvarkit\wgscoverageplotter\main.nf line 29:

    -R ${fasta} \
       ^------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -R "${fasta}" \

In .\modules\nf-core\jvarkit\wgscoverageplotter\main.nf line 30:

    ${args} \
    ^-----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${args}" \

In .\modules\nf-core\jvarkit\wgscoverageplotter\main.nf line 31:

    ${bam} > "${prefix}.svg"
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "${bam}" > "${prefix}.svg"

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...

ShellCheck results for .\modules\nf-core\kaiju\kaiju\main.nf:

In .\modules\nf-core\kaiju\kaiju\main.nf line 26:

dbnodes=`find -L ${db} -name "*nodes.dmp"`
^-----^ SC2034 (warning): dbnodes appears unused. Verify use (or export if used externally).
        ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.
                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
dbnodes=$(find -L "${db}" -name "*nodes.dmp")

In .\modules\nf-core\kaiju\kaiju\main.nf line 27:

dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
^----^ SC2034 (warning): dbname appears unused. Verify use (or export if used externally).
       ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.
                ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
dbname=$(find -L "${db}" -name "*.fmi" -not -name "._*")

In .\modules\nf-core\kaiju\kaiju\main.nf line 29:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\kaiju\kaiju\main.nf line 30:

    -z $task.cpus \
       ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -z "$task".cpus \

In .\modules\nf-core\kaiju\kaiju\main.nf line 33:

    -o ${prefix}.tsv \
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".tsv \

In .\modules\nf-core\kaiju\kaiju\main.nf line 34:

    $input
    ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$input"

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- dbname appears unused. Verify use...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\kaiju\kaiju2krona\main.nf:

In .\modules\nf-core\kaiju\kaiju2krona\main.nf line 25:

dbnodes=`find -L ${db} -name "*nodes.dmp"`
^-----^ SC2034 (warning): dbnodes appears unused. Verify use (or export if used externally).
        ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.
                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
dbnodes=$(find -L "${db}" -name "*nodes.dmp")

In .\modules\nf-core\kaiju\kaiju2krona\main.nf line 26:

dbnames=`find -L ${db} -name "*names.dmp"`
^-----^ SC2034 (warning): dbnames appears unused. Verify use (or export if used externally).
        ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.
                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
dbnames=$(find -L "${db}" -name "*names.dmp")

In .\modules\nf-core\kaiju\kaiju2krona\main.nf line 28:

    $args \
    ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    "$args" \

In .\modules\nf-core\kaiju\kaiju2krona\main.nf line 31:

    -i ${tsv} \
       ^----^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -i "${tsv}" \

In .\modules\nf-core\kaiju\kaiju2krona\main.nf line 32:

    -o ${prefix}.txt
       ^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
    -o "${prefix}".txt

For more information:
  https://www.shellcheck.net/wiki/SC2034 -- dbnames appears unused. Verify us...
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

ShellCheck results for .\modules\nf-core\kaiju\kaiju2table\main.nf:

In .\modules\nf-core\kaiju\kaiju2table\main.nf line 26:

dbnodes=`find -L ${db} -name "*nodes.dmp"`
^-----^ SC2034 (warning): dbnodes appears unused. Verify use (or export if used externally).
        ^-- SC2006 (style): Use $(...) notation instead of legacy backticks `...`.
                 ^---^ SC2086 (info): Double quote to prevent globbing and word splitting.

Did you mean: 
dbnodes=$(find -L "${db}" -name "*nodes.dmp")

In .\modules\nf-core\kaiju\kaiju2table\main.nf line 27:

dbnames=`find -L ${db} -name "*names.dmp"`
^-----^ SC2034 (warning): dbnames appears unused. Verify use