A script to run ffmpeg on all the files in a folder and remux videos also you can add other files in the sec folder

ffmpeg.sh

#!/bin/bash
set -e

# Set input and output file extensions and additional ffmpeg arguments here
input_ext="mkv"           # Input file extension (e.g., mp4, mkv) without the dot
output_ext="mkv"          # Output file extension (e.g., mp4, mkv) without the dot

# Create the output directory if it doesn't exist
output_dir="$PWD/dir"
mkdir -p "$output_dir"

# Get the list of input files in the current directory
input_dir="$PWD"
sec_dir="$PWD/sec"

# Get a list of files with the specified input extension in the input directory
input_files=("$input_dir"/*."$input_ext")

# Check if the sec directory exists and get the list of files in the sec directory if it does
if [ -d "$sec_dir" ]; then
    sec_files=("$sec_dir"/*."$input_ext")
else
    echo "Warning: The '$sec_dir' directory does not exist. Only input files will be processed."
    sec_files=()  # If sec doesn't exist, set sec_files to an empty array
fi

# Check if the number of input files match with sec files (if sec directory exists)
if [ ${#sec_files[@]} -gt 0 ] && [ ${#input_files[@]} -ne ${#sec_files[@]} ]; then
    echo "Error: The number of files in $input_dir and $sec_dir do not match."
    exit 1
fi

# Process each input file
for ((i=0; i<${#input_files[@]}; i++)); do
    input_file="${input_files[$i]}"
    
    # If sec directory exists, use the corresponding sec file
    if [ ${#sec_files[@]} -gt 0 ]; then
        sec_file="${sec_files[$i]}"
    else
        sec_file=""  # No corresponding sec file if sec doesn't exist
    fi

    # Get the filename without extension for output naming
    filename=$(basename "$input_file" ."$input_ext")

    # Example ffmpeg arguments (can be customized)
    ffmpeg_args=(-c:v copy -c:a copy -c:s copy -map 0:v:m:language:eng -map 0:a:m:language:eng -map 0:s:m:language:eng -metadata title=${filename:0})    

    # Construct the output file name with the desired extension in the 'dir' folder
    output_file="$output_dir/$filename.$output_ext"

    # Run ffmpeg with the chosen arguments
    if [ -z "$sec_file" ]; then
        # If sec file doesn't exist, process only the input file
        echo "Processing: $input_file -> $output_file"
        ffmpeg -i "$input_file" "${ffmpeg_args[@]}" -y "$output_file"
    else
        # If sec file exists, process both input and sec files
        echo "Processing: $input_file + $sec_file -> $output_file"
        ffmpeg -i "$input_file" -i "$sec_file" "${ffmpeg_args[@]}" -y "$output_file"
    fi
done

echo "Processing complete. Output files are in '$output_dir'."