nf-core_modules/modules/subread/featurecounts/main.nf
2022-02-04 09:53:32 +01:00

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