2020-09-10 15:45:11 +00:00
|
|
|
// Import generic module functions
|
2021-09-27 08:41:24 +00:00
|
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
2020-09-10 15:45:11 +00:00
|
|
|
|
2020-10-14 17:29:50 +00:00
|
|
|
params.options = [:]
|
2021-03-15 12:16:43 +00:00
|
|
|
options = initOptions(params.options)
|
2020-10-14 17:29:50 +00:00
|
|
|
|
2020-09-10 15:45:11 +00:00
|
|
|
process SUBREAD_FEATURECOUNTS {
|
|
|
|
tag "$meta.id"
|
|
|
|
label 'process_medium'
|
|
|
|
publishDir "${params.outdir}",
|
|
|
|
mode: params.publish_dir_mode,
|
2021-04-09 16:23:56 +00:00
|
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
2020-10-14 17:29:50 +00:00
|
|
|
|
2021-02-16 23:58:23 +00:00
|
|
|
conda (params.enable_conda ? "bioconda::subread=2.0.1" : null)
|
2020-12-13 23:41:53 +00:00
|
|
|
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"
|
|
|
|
}
|
2020-09-10 15:45:11 +00:00
|
|
|
|
|
|
|
input:
|
|
|
|
tuple val(meta), path(bams), path(annotation)
|
2020-12-17 23:50:24 +00:00
|
|
|
|
2020-09-10 15:45:11 +00:00
|
|
|
output:
|
|
|
|
tuple val(meta), path("*featureCounts.txt") , emit: counts
|
|
|
|
tuple val(meta), path("*featureCounts.txt.summary"), emit: summary
|
2021-09-27 08:41:24 +00:00
|
|
|
path "versions.yml" , emit: version
|
2020-09-10 15:45:11 +00:00
|
|
|
|
|
|
|
script:
|
|
|
|
def software = getSoftwareName(task.process)
|
2020-10-14 17:29:50 +00:00
|
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
2020-09-10 15:45:11 +00:00
|
|
|
def paired_end = meta.single_end ? '' : '-p'
|
|
|
|
|
|
|
|
def strandedness = 0
|
|
|
|
if (meta.strandedness == 'forward') {
|
|
|
|
strandedness = 1
|
|
|
|
} else if (meta.strandedness == 'reverse') {
|
|
|
|
strandedness = 2
|
|
|
|
}
|
|
|
|
"""
|
|
|
|
featureCounts \\
|
2020-10-14 17:29:50 +00:00
|
|
|
$options.args \\
|
2020-09-10 15:45:11 +00:00
|
|
|
$paired_end \\
|
|
|
|
-T $task.cpus \\
|
|
|
|
-a $annotation \\
|
|
|
|
-s $strandedness \\
|
|
|
|
-o ${prefix}.featureCounts.txt \\
|
|
|
|
${bams.join(' ')}
|
|
|
|
|
2021-09-27 08:41:24 +00:00
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
|
|
${getProcessName(task.process)}:
|
2021-09-28 19:25:10 +00:00
|
|
|
${getSoftwareName(task.process)}: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
|
2021-09-27 08:41:24 +00:00
|
|
|
END_VERSIONS
|
2020-09-10 15:45:11 +00:00
|
|
|
"""
|
|
|
|
}
|