mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 23:43:19 -05:00
dce27b8102
* Update functions.nf * Replace saveAs line in module main script * Add spacing for ECLint
35 lines
1.2 KiB
Text
35 lines
1.2 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process GUNZIP {
|
|
tag "$archive"
|
|
label 'process_low'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
|
|
|
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
|
|
} else {
|
|
container "biocontainers/biocontainers:v1.2.0_cv1"
|
|
}
|
|
|
|
input:
|
|
path archive
|
|
|
|
output:
|
|
path "$gunzip", emit: gunzip
|
|
path "*.version.txt", emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
gunzip = archive.toString() - '.gz'
|
|
"""
|
|
gunzip -f $options.args $archive
|
|
echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|