nf-core_modules/modules/untar/main.nf
Harshil Patel 3c5492b4a3
Fix more version commands (#750)
* Fix outstanding tests

* Fix more version commands

* Fix remaining modules
2021-09-28 06:56:27 +01:00

42 lines
1.3 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process UNTAR {
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 "$untar" , emit: untar
path "versions.yml", emit: version
script:
def software = getSoftwareName(task.process)
untar = archive.toString() - '.tar.gz'
"""
tar \\
-xzvf \\
$options.args \\
$archive
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS
"""
}