nf-core_modules/modules/untar/main.nf
2022-06-02 11:09:55 +02:00

53 lines
1.3 KiB
Text

process UNTAR {
tag "$archive"
label 'process_low'
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
input:
tuple val(meta), path(archive)
output:
tuple val(meta), path("$untar"), emit: untar
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
untar = archive.toString() - '.tar.gz'
"""
mkdir output
tar \\
-C output --strip-components 1 \\
-xzvf \\
$args \\
$archive \\
$args2
mv output ${untar}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS
"""
stub:
untar = archive.toString() - '.tar.gz'
"""
touch $untar
cat <<-END_VERSIONS > versions.yml
"${task.process}":
untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS
"""
}