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Update featurecounts module
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1 changed files with 13 additions and 5 deletions
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@ -15,24 +15,32 @@ process SUBREAD_FEATURECOUNTS {
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input:
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tuple val(meta), path(bams), path(annotation)
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val options
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val options
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output:
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tuple val(meta), path("*featureCounts.txt"), emit: txt
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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 "*.version.txt", emit: version
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def pe = meta.single_end ? '' : '-p'
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def strandedness = 0
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if (meta.strandedness == 'forward') {
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strandedness = 1
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} else if (meta.strandedness == 'reverse') {
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strandedness = 2
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}
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def paired_end = meta.single_end ? '' : '-p'
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"""
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featureCounts \\
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$ioptions.args \\
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$pe \\
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$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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