nf-core_modules/modules/subread/featurecounts/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process SUBREAD_FEATURECOUNTS {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::subread=2.0.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
} else {
container "quay.io/biocontainers/subread:2.0.1--hed695b0_0"
}
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input:
tuple val(meta), path(bams), path(annotation)
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output:
tuple val(meta), path("*featureCounts.txt") , emit: counts
tuple val(meta), path("*featureCounts.txt.summary"), emit: summary
path "versions.yml" , emit: version
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script:
def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def paired_end = meta.single_end ? '' : '-p'
def strandedness = 0
if (meta.strandedness == 'forward') {
strandedness = 1
} else if (meta.strandedness == 'reverse') {
strandedness = 2
}
"""
featureCounts \\
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$options.args \\
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$paired_end \\
-T $task.cpus \\
-a $annotation \\
-s $strandedness \\
-o ${prefix}.featureCounts.txt \\
${bams.join(' ')}
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
END_VERSIONS
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"""
}