nf-core_modules/modules/gunzip/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process GUNZIP {
tag "$archive"
label 'process_low'
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publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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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
"""
}