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48 lines
1.4 KiB
Plaintext
48 lines
1.4 KiB
Plaintext
process SUBREAD_FEATURECOUNTS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::subread=2.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' :
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'quay.io/biocontainers/subread:2.0.1--hed695b0_0' }"
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input:
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tuple val(meta), path(bams), path(annotation)
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output:
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tuple val(meta), path("*featureCounts.txt") , emit: counts
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tuple val(meta), path("*featureCounts.txt.summary"), emit: summary
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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 prefix = task.ext.prefix ?: "${meta.id}"
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def paired_end = meta.single_end ? '' : '-p'
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def strandedness = 0
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if (meta.strandedness == 'forward') {
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strandedness = 1
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} else if (meta.strandedness == 'reverse') {
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strandedness = 2
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}
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"""
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featureCounts \\
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$args \\
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$paired_end \\
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-T $task.cpus \\
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-a $annotation \\
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-s $strandedness \\
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-o ${prefix}.featureCounts.txt \\
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${bams.join(' ')}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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subread: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
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END_VERSIONS
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"""
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}
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