2020-09-10 15:45:11 +00:00
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// Import generic module functions
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2021-09-27 08:41:24 +00:00
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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2020-09-10 15:45:11 +00:00
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2020-10-14 17:29:50 +00:00
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params.options = [:]
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2021-03-15 12:16:43 +00:00
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options = initOptions(params.options)
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2020-10-14 17:29:50 +00:00
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2020-09-10 15:45:11 +00:00
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process SUBREAD_FEATURECOUNTS {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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2021-04-09 16:23:56 +00:00
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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2020-10-14 17:29:50 +00:00
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2021-02-16 23:58:23 +00:00
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conda (params.enable_conda ? "bioconda::subread=2.0.1" : null)
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2020-12-13 23:41:53 +00:00
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
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} else {
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container "quay.io/biocontainers/subread:2.0.1--hed695b0_0"
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}
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2020-09-10 15:45:11 +00:00
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input:
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tuple val(meta), path(bams), path(annotation)
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2020-12-17 23:50:24 +00:00
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2020-09-10 15:45:11 +00:00
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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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2021-10-01 13:04:56 +00:00
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path "versions.yml" , emit: versions
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2020-09-10 15:45:11 +00:00
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script:
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2020-10-14 17:29:50 +00:00
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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2020-09-10 15:45:11 +00:00
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def paired_end = meta.single_end ? '' : '-p'
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def strandedness = 0
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if (meta.strandedness == 'forward') {
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strandedness = 1
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} else if (meta.strandedness == 'reverse') {
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strandedness = 2
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}
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"""
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featureCounts \\
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2020-10-14 17:29:50 +00:00
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$options.args \\
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2020-09-10 15:45:11 +00:00
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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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2021-09-27 08:41:24 +00:00
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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2021-09-28 19:25:10 +00:00
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${getSoftwareName(task.process)}: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
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2021-09-27 08:41:24 +00:00
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END_VERSIONS
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2020-09-10 15:45:11 +00:00
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"""
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}
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