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96 lines
3.1 KiB
Plaintext
96 lines
3.1 KiB
Plaintext
process CHROMAP_CHROMAP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::chromap=0.1.5 bioconda::samtools=1.14" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' :
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'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' }"
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input:
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tuple val(meta), path(reads)
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path fasta
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path index
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path barcodes
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path whitelist
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path chr_order
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path pairs_chr_order
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output:
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tuple val(meta), path("*.bed.gz") , optional:true, emit: bed
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tuple val(meta), path("*.bam") , optional:true, emit: bam
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tuple val(meta), path("*.tagAlign.gz"), optional:true, emit: tagAlign
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tuple val(meta), path("*.pairs.gz") , optional:true, emit: pairs
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def args_list = args.tokenize()
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def file_extension = args.contains("--SAM") ? 'sam' : args.contains("--TagAlign")? 'tagAlign' : args.contains("--pairs")? 'pairs' : 'bed'
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if (barcodes) {
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args_list << "-b ${barcodes.join(',')}"
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if (whitelist) {
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args_list << "--barcode-whitelist $whitelist"
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}
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}
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if (chr_order) {
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args_list << "--chr-order $chr_order"
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}
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if (pairs_chr_order){
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args_list << "--pairs-natural-chr-order $pairs_chr_order"
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}
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def final_args = args_list.join(' ')
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def compression_cmds = "gzip -n ${prefix}.${file_extension}"
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if (args.contains("--SAM")) {
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compression_cmds = """
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samtools view $args2 -@ $task.cpus -bh \\
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-o ${prefix}.bam ${prefix}.${file_extension}
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rm ${prefix}.${file_extension}
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"""
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}
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if (meta.single_end) {
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"""
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chromap \\
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$final_args \\
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-t $task.cpus \\
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-x $index \\
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-r $fasta \\
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-1 ${reads.join(',')} \\
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-o ${prefix}.${file_extension}
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$compression_cmds
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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chromap: \$(echo \$(chromap --version 2>&1))
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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} else {
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"""
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chromap \\
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$final_args \\
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-t $task.cpus \\
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-x $index \\
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-r $fasta \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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-o ${prefix}.${file_extension}
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$compression_cmds
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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chromap: \$(echo \$(chromap --version 2>&1))
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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}
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