mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
52 lines
1.8 KiB
Text
52 lines
1.8 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
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']) }
|
|
|
|
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"
|
|
}
|
|
|
|
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 "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.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 \\
|
|
$options.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
|
|
"""
|
|
}
|