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stain/ro-crate-metadata.json

Created April 14, 2021 12:49
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ro-crate-metadata.json
{
"@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"about": {
"@id": "./"
},
"conformsTo": {
"@id": "https://w3id.org/ro/crate/1.1"
}
},
{
"@id": "ro-crate-preview.html",
"@type": "CreativeWork",
"about": {
"@id": "./"
}
},
{
"@id": "./",
"@type": "Dataset",
"mainEntity": {
"@id": "workflow.cwl"
},
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{
"@id": "workflow.cwl"
},
{
"@id": "workflow-diagram-147-1.svg"
}
],
"identifier": "https://dev.workflowhub.eu/workflows/147?version=1",
"url": "https://dev.workflowhub.eu/workflows/147/ro_crate?version=1",
"name": "Research Object Crate for exome-alignment",
"description": "",
"isBasedOn": "https://github.com/inab/ipc_workflows/blob/main/exome/alignment/workflow.cwl",
"sdDatePublished": "2021-04-14 13:45:56 +0100",
"creativeWorkStatus": "Stable"
},
{
"@id": "workflow.cwl",
"@type": [
"File",
"SoftwareSourceCode",
"ComputationalWorkflow"
],
"programmingLanguage": {
"@id": "#cwl"
},
"url": "https://github.com/inab/ipc_workflows/blob/main/exome/alignment/workflow.cwl",
"contentSize": 2517,
"image": {
"@id": "workflow-diagram-147-1.svg"
},
"description": "",
"name": "exome-alignment",
"keywords": "",
"license": "https://opensource.org/licenses/Apache-2.0",
"creator": {
"@id": "https://dev.workflowhub.eu/people/11"
},
"producer": {
"@id": "https://dev.workflowhub.eu/projects/15"
},
"dateCreated": {
"@value": "2021-03-03T15:16:34Z",
"@type": "http://www.w3.org/2001/XMLSchema#dateTime"
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"@value": "2021-03-03T15:17:31Z",
"@type": "http://www.w3.org/2001/XMLSchema#dateTime"
},
"sdPublisher": {
"@id": "https://dev.workflowhub.eu"
},
"version": 1,
"input": [
{
"@id": "#exome_alignment-inputs-fastq_files"
},
{
"@id": "#exome_alignment-inputs-reference_genome"
},
{
"@id": "#exome_alignment-inputs-readgroup_str"
},
{
"@id": "#exome_alignment-inputs-sample_name"
}
],
"output": {
"@id": "#exome_alignment-outputs-md_bam"
},
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/"
},
{
"@id": "workflow-diagram-147-1.svg",
"@type": [
"File",
"ImageObject",
"WorkflowSketch"
],
"contentSize": 9994
},
{
"@id": "https://dev.workflowhub.eu/people/11",
"@type": "Person",
"name": "Laura Rodriguez-Navas"
},
{
"@id": "https://dev.workflowhub.eu/projects/15",
"@type": [
"Project",
"Organization"
],
"name": "iPC: individualizedPaediatricCure"
},
{
"@id": "https://dev.workflowhub.eu",
"@type": "Organization",
"name": "WorkflowHub",
"url": "https://dev.workflowhub.eu"
},
{
"@id": "#cwl",
"@type": "ComputerLanguage",
"name": "Common Workflow Language",
"alternateName": "CWL",
"identifier": {
"@id": "https://w3id.org/cwl/v1.0/"
},
"url": {
"@id": "https://www.commonwl.org/"
}
},
{
"@id": "#exome_alignment-inputs-fastq_files",
"@type": "FormalParameter",
"name": "fastq_files",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@id": "#exome_alignment-inputs-reference_genome",
"@type": "FormalParameter",
"name": "reference_genome",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@id": "#exome_alignment-inputs-readgroup_str",
"@type": "FormalParameter",
"name": "readgroup_str",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@id": "#exome_alignment-inputs-sample_name",
"@type": "FormalParameter",
"name": "sample_name",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@id": "#exome_alignment-outputs-md_bam",
"@type": "FormalParameter",
"name": "md_bam",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
}
]
}
Raw
ro-crate-preview.html
<html>
<head>
<script type="application/ld+json">
{
"@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"about": {
"@id": "./"
},
"conformsTo": {
"@id": "https://w3id.org/ro/crate/1.1"
}
},
{
"@id": "ro-crate-preview.html",
"@type": "CreativeWork",
"about": {
"@id": "./"
}
},
{
"@id": "./",
"@type": "Dataset",
"mainEntity": {
"@id": "workflow.cwl"
},
"hasPart": [
{
"@id": "workflow.cwl"
},
{
"@id": "workflow-diagram-147-1.svg"
}
],
"identifier": "https://dev.workflowhub.eu/workflows/147?version=1",
"url": "https://dev.workflowhub.eu/workflows/147/ro_crate?version=1",
"name": "Research Object Crate for exome-alignment",
"description": "",
"isBasedOn": "https://github.com/inab/ipc_workflows/blob/main/exome/alignment/workflow.cwl",
"sdDatePublished": "2021-04-14 13:45:56 +0100",
"creativeWorkStatus": "Stable",
"@reverse": {
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{
"@id": "ro-crate-metadata.json"
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{
"@id": "ro-crate-preview.html"
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},
{
"@id": "workflow.cwl",
"@type": [
"File",
"SoftwareSourceCode",
"ComputationalWorkflow"
],
"programmingLanguage": {
"@id": "#cwl"
},
"url": "https://github.com/inab/ipc_workflows/blob/main/exome/alignment/workflow.cwl",
"contentSize": 2517,
"image": {
"@id": "workflow-diagram-147-1.svg"
},
"description": "",
"name": "exome-alignment",
"keywords": "",
"license": "https://opensource.org/licenses/Apache-2.0",
"creator": {
"@id": "https://dev.workflowhub.eu/people/11"
},
"producer": {
"@id": "https://dev.workflowhub.eu/projects/15"
},
"dateCreated": {
"@value": "2021-03-03T15:16:34Z",
"@type": "http://www.w3.org/2001/XMLSchema#dateTime"
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"@type": "http://www.w3.org/2001/XMLSchema#dateTime"
},
"sdPublisher": {
"@id": "https://dev.workflowhub.eu"
},
"version": 1,
"input": [
{
"@id": "#exome_alignment-inputs-fastq_files"
},
{
"@id": "#exome_alignment-inputs-reference_genome"
},
{
"@id": "#exome_alignment-inputs-readgroup_str"
},
{
"@id": "#exome_alignment-inputs-sample_name"
}
],
"output": {
"@id": "#exome_alignment-outputs-md_bam"
},
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
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],
"contentSize": 9994,
"@reverse": {
"hasPart": [
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}
],
"image": [
{
"@id": "workflow.cwl"
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]
}
},
{
"@id": "https://dev.workflowhub.eu/people/11",
"@type": "Person",
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},
{
"@id": "https://dev.workflowhub.eu",
"@type": "Organization",
"name": "WorkflowHub",
"url": "https://dev.workflowhub.eu",
"@reverse": {
"sdPublisher": [
{
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}
]
}
},
{
"@id": "#cwl",
"@type": "ComputerLanguage",
"name": "Common Workflow Language",
"alternateName": "CWL",
"identifier": {
"@id": "https://w3id.org/cwl/v1.0/"
},
"url": {
"@id": "https://www.commonwl.org/"
},
"@reverse": {
"programmingLanguage": [
{
"@id": "workflow.cwl"
}
]
}
},
{
"@id": "#exome_alignment-inputs-fastq_files",
"@type": "FormalParameter",
"name": "fastq_files",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/",
"@reverse": {
"input": [
{
"@id": "workflow.cwl"
}
]
}
},
{
"@id": "#exome_alignment-inputs-reference_genome",
"@type": "FormalParameter",
"name": "reference_genome",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/",
"@reverse": {
"input": [
{
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}
]
}
},
{
"@id": "#exome_alignment-inputs-readgroup_str",
"@type": "FormalParameter",
"name": "readgroup_str",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/",
"@reverse": {
"input": [
{
"@id": "workflow.cwl"
}
]
}
},
{
"@id": "#exome_alignment-inputs-sample_name",
"@type": "FormalParameter",
"name": "sample_name",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/",
"@reverse": {
"input": [
{
"@id": "workflow.cwl"
}
]
}
},
{
"@id": "#exome_alignment-outputs-md_bam",
"@type": "FormalParameter",
"name": "md_bam",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/",
"@reverse": {
"output": [
{
"@id": "workflow.cwl"
}
]
}
}
]
}
</script>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
<script src="https://data.research.uts.edu.au/examples/ro-crate/examples/src/crate.js"></script>
<link rel="stylesheet"
href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
crossorigin="anonymous"/>
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">
<meta charset='utf-8'/>
<style>
table.table {
padding-bottom: 300px;
}
</style>
</head>
<body>
<nav class="navbar">
<ul class="nav navbar-nav" >
<li ><a href="#"><span class="glyphicon glyphicon-home dataset_name">&nbsp;Research Object Crate for exome-alignment</span></a></li>
</ul>
</nav>
<div class="container">
<div class="jumbotron">
<h4 class="citation"></h3>
<h3 class="item_name">Research Object Crate for exome-alignment</h4>
<a href="./ro-crate-metadata.json">⬇️🏷️ Download all the metadata for <span class='name'>Research Object Crate for exome-alignment</span> in JSON-LD format</a>
<div class="check"></div>
</div>
<div id="summary">
<div><h3></h3><table class="table metadata table-striped" id="./"><tbody><tr><th style="white-space: nowrap; width: 1%;">name<span>&nbsp;</span><a href="http://schema.org/name">[?]</a></th><td style="text-align:left"> <span>Research Object Crate for exome-alignment</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">@type</th><td style="text-align:left"> <span>Dataset</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">description<span>&nbsp;</span><a href="http://schema.org/description">[?]</a></th><td style="text-align:left"> <ul></ul></td></tr><tr><th style="white-space: nowrap;">Referenced by</th><td style="text-align:left"> <tbody><tr><th style="white-space: nowrap; width: 1%;">about<span>&nbsp;</span><a href="http://schema.org/about">[?]</a></th><td style="text-align:left"> <ul><li><a href="#ro-crate-metadata.json">ro-crate-metadata.json</a></li><li><a href="#ro-crate-preview.html">ro-crate-preview.html</a></li></ul></td></tr></tbody></td></tr><tr><th style="white-space: nowrap; width: 1%;">mainEntity<span>&nbsp;</span><a href="http://schema.org/mainEntity">[?]</a></th><td style="text-align:left"> <a href="#workflow.cwl">exome-alignment</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">hasPart<span>&nbsp;</span><a href="http://schema.org/hasPart">[?]</a></th><td style="text-align:left"> <ul><li><a href="#workflow.cwl">exome-alignment</a></li><li><a href="#workflow-diagram-147-1.svg">workflow-diagram-147-1.svg</a></li></ul></td></tr><tr><th style="white-space: nowrap; width: 1%;">identifier<span>&nbsp;</span><a href="http://schema.org/identifier">[?]</a></th><td style="text-align:left"> <a href="https://dev.workflowhub.eu/workflows/147?version=1">https://dev.workflowhub.eu/workflows/147?version=1</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">url<span>&nbsp;</span><a href="http://schema.org/url">[?]</a></th><td style="text-align:left"> <a href="https://dev.workflowhub.eu/workflows/147/ro_crate?version=1">https://dev.workflowhub.eu/workflows/147/ro_crate?version=1</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">isBasedOn<span>&nbsp;</span><a href="http://schema.org/isBasedOn">[?]</a></th><td style="text-align:left"> <a href="https://github.com/inab/ipc_workflows/blob/main/exome/alignment/workflow.cwl">https://github.com/inab/ipc_workflows/blob/main/exome/alignment/workflow.cwl</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">sdDatePublished<span>&nbsp;</span><a href="http://schema.org/sdDatePublished">[?]</a></th><td style="text-align:left"> <span>2021-04-14 13:45:56 +0100</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">creativeWorkStatus<span>&nbsp;</span><a href="http://schema.org/creativeWorkStatus">[?]</a></th><td style="text-align:left"> <span>Stable</span></td></tr></tbody></table></div><div><h3><a href="workflow.cwl">⬇️ Download: workflow.cwl</a></h3><table class="table metadata table-striped" id="workflow.cwl"><tbody><tr><th style="white-space: nowrap; width: 1%;">name<span>&nbsp;</span><a href="http://schema.org/name">[?]</a></th><td style="text-align:left"> <span>exome-alignment</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">@type</th><td style="text-align:left"> <ul><li><span>File</span></li><li><span>SoftwareSourceCode</span></li><li><span>ComputationalWorkflow</span></li></ul></td></tr><tr><th style="white-space: nowrap; width: 1%;">description<span>&nbsp;</span><a href="http://schema.org/description">[?]</a></th><td style="text-align:left"> <ul></ul></td></tr><tr><th style="white-space: nowrap; width: 1%;">contentSize<span>&nbsp;</span><a href="http://schema.org/contentSize">[?]</a></th><td style="text-align:left"> <span>2517</span></td></tr><tr><th style="white-space: nowrap;">Referenced by</th><td style="text-align:left"> <tbody><tr><th style="white-space: nowrap; width: 1%;">mainEntity<span>&nbsp;</span><a href="http://schema.org/mainEntity">[?]</a></th><td style="text-align:left"> <a href="#./">Research Object Crate for exome-alignment</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">hasPart<span>&nbsp;</span><a href="http://schema.org/hasPart">[?]</a></th><td style="text-align:left"> <a href="#./">Research Object Crate for exome-alignment</a></td></tr></tbody></td></tr><tr><th style="white-space: nowrap; width: 1%;">programmingLanguage<span>&nbsp;</span><a href="http://schema.org/programmingLanguage">[?]</a></th><td style="text-align:left"> <a href="##cwl">Common Workflow Language</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">url<span>&nbsp;</span><a href="http://schema.org/url">[?]</a></th><td style="text-align:left"> <a href="https://github.com/inab/ipc_workflows/blob/main/exome/alignment/workflow.cwl">https://github.com/inab/ipc_workflows/blob/main/exome/alignment/workflow.cwl</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">image<span>&nbsp;</span><a href="http://schema.org/image">[?]</a></th><td style="text-align:left"> <a href="#workflow-diagram-147-1.svg">workflow-diagram-147-1.svg</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">keywords<span>&nbsp;</span><a href="http://schema.org/keywords">[?]</a></th><td style="text-align:left"> <ul></ul></td></tr><tr><th style="white-space: nowrap; width: 1%;">license<span>&nbsp;</span><a href="http://schema.org/license">[?]</a></th><td style="text-align:left"> <a href="https://opensource.org/licenses/Apache-2.0">https://opensource.org/licenses/Apache-2.0</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">creator<span>&nbsp;</span><a href="http://schema.org/creator">[?]</a></th><td style="text-align:left"> <a href="#https://dev.workflowhub.eu/people/11">Laura Rodriguez-Navas</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">producer<span>&nbsp;</span><a href="http://schema.org/producer">[?]</a></th><td style="text-align:left"> <a href="#https://dev.workflowhub.eu/projects/15">iPC: individualizedPaediatricCure</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">dateCreated<span>&nbsp;</span><a href="http://schema.org/dateCreated">[?]</a></th><td style="text-align:left"> <span>[object Object]</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">dateModified<span>&nbsp;</span><a href="http://schema.org/dateModified">[?]</a></th><td style="text-align:left"> <span>[object Object]</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">sdPublisher<span>&nbsp;</span><a href="http://schema.org/sdPublisher">[?]</a></th><td style="text-align:left"> <a href="#https://dev.workflowhub.eu">WorkflowHub</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">version<span>&nbsp;</span><a href="http://schema.org/version">[?]</a></th><td style="text-align:left"> <span>1</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">input<span>&nbsp;</span><a href="https://bioschemas.org/ComputationalWorkflow#input">[?]</a></th><td style="text-align:left"> <ul><li><a href="##exome_alignment-inputs-fastq_files">fastq_files</a></li><li><a href="##exome_alignment-inputs-reference_genome">reference_genome</a></li><li><a href="##exome_alignment-inputs-readgroup_str">readgroup_str</a></li><li><a href="##exome_alignment-inputs-sample_name">sample_name</a></li></ul></td></tr><tr><th style="white-space: nowrap; width: 1%;">output<span>&nbsp;</span><a href="https://bioschemas.org/ComputationalWorkflow#output">[?]</a></th><td style="text-align:left"> <a href="##exome_alignment-outputs-md_bam">md_bam</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">dct:conformsTo</th><td style="text-align:left"> <a href="https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/">https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/</a></td></tr></tbody></table></div><div><h3><a href="workflow-diagram-147-1.svg">⬇️ Download: workflow-diagram-147-1.svg</a></h3><table class="table metadata table-striped" id="workflow-diagram-147-1.svg"><tbody><tr><th style="white-space: nowrap; width: 1%;">@type</th><td style="text-align:left"> <ul><li><span>File</span></li><li><span>ImageObject</span></li><li><span>WorkflowSketch</span></li></ul></td></tr><tr><th style="white-space: nowrap; width: 1%;">contentSize<span>&nbsp;</span><a href="http://schema.org/contentSize">[?]</a></th><td style="text-align:left"> <span>9994</span></td></tr><tr><th style="white-space: nowrap;">Referenced by</th><td style="text-align:left"> <tbody><tr><th style="white-space: nowrap; width: 1%;">hasPart<span>&nbsp;</span><a href="http://schema.org/hasPart">[?]</a></th><td style="text-align:left"> <a href="#./">Research Object Crate for exome-alignment</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">image<span>&nbsp;</span><a href="http://schema.org/image">[?]</a></th><td style="text-align:left"> <a href="#workflow.cwl">exome-alignment</a></td></tr></tbody></td></tr></tbody></table></div>
</div>
<p>This file was created at 1618404404134 by
<a href='https://code.research.uts.edu.au/eresearch/calcytejs'>
Calcyte</a> which implements the <a href=''>
Draft RO-Crate format</a>, version
</p>
</body>
</html>
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workflow-diagram-147-1.svg
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workflow.cwl
class: Workflow
cwlVersion: v1.0
label: align-workflow
requirements:
- class: MultipleInputFeatureRequirement
$namespaces:
s: https://schema.org/
edam: http://edamontology.org/
$schemas:
- https://schema.org/version/latest/schemaorg-current-https.rdf
- http://edamontology.org/EDAM_1.18.owl
inputs:
fastq_files: {type: 'File[]', doc: "List of paired-end input FASTQ files"}
reference_genome: {type: File, doc: "Compress FASTA files with the reference genome chromosomes"}
readgroup_str: {type: string, default: '@RG\tID:Seq01p\tSM:Seq01\tPL:ILLUMINA\tPI:330', doc: "Parsing header which should correlate to FASTQ files"}
sample_name: {type: string, default: 'ABC3', doc: "Sample name"}
outputs:
md_bam: {type: File, outputSource: picard_markduplicates/md_bam, doc: ""}
steps:
gunzip:
run: tools/gunzip.cwl
in:
reference_file: reference_genome
out: [unzipped_fasta]
picard_dictionary:
run: tools/picard_dictionary.cwl
in:
reference_genome:
source: gunzip/unzipped_fasta
out: [dict]
cutadapt:
run: tools/cutadapt.cwl
in:
raw_sequences: fastq_files
out: [trimmed_fastq]
bwa_index:
run: tools/bwa-index.cwl
in:
reference_genome:
source: gunzip/unzipped_fasta
out: [output]
samtools_index:
run: tools/samtools_index.cwl
in:
input:
source: gunzip/unzipped_fasta
out: [index_fai]
bwa_mem:
run: tools/bwa-mem.cwl
in:
sample_name: sample_name
trimmed_fastq:
source: cutadapt/trimmed_fastq
read_group: readgroup_str
reference_genome:
source: bwa_index/output
out: [aligned_sam]
samtools_sort:
run: tools/samtools_sort_bam.cwl
in:
input:
source: bwa_mem/aligned_sam
out: [sorted_bam]
picard_markduplicates:
run: tools/picard_markduplicates.cwl
in:
input:
source: samtools_sort/sorted_bam
out: [md_bam]
s:author:
- class: s:Person
s:identifier: https://orcid.org/0000-0003-4929-1219
s:email: mailto:[email protected]
s:name: Laura Rodríguez-Navas
s:dateCreated: "2021-02-19"
s:license: https://spdx.org/licenses/Apache-2.0
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