nf-core_modules/software/subread/featurecounts/main.nf
2020-09-10 16:45:11 +01:00

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