mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
33 lines
1.1 KiB
Text
33 lines
1.1 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
def options = initOptions(params.options)
|
|
|
|
process GFFREAD {
|
|
tag "$gff"
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
|
|
|
conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0"
|
|
} else {
|
|
container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
|
|
}
|
|
|
|
input:
|
|
path gff
|
|
|
|
output:
|
|
path "*.gtf" , emit: gtf
|
|
path "*.version.txt", emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
"""
|
|
gffread $gff $options.args -o ${gff.baseName}.gtf
|
|
echo \$(gffread --version 2>&1) > ${software}.version.txt
|
|
"""
|
|
}
|