nf-core_modules/modules/unzip/main.nf
James A. Fellows Yates e080f4c8ac
Untar unzip meta (#1408)
* fix: remove left-over unnecessary code

* Adds support for meta lists for unzip and untar

* Fix test inputs

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Fix MALTEXTRACT/AMPS

* Fix further modules

* Fix cellranger

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-03-21 14:49:28 +01:00

35 lines
1.1 KiB
Text

process UNZIP {
tag "$archive"
label 'process_low'
conda (params.enable_conda ? "bioconda::p7zip=15.09" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/p7zip:15.09--h2d50403_4' :
'quay.io/biocontainers/p7zip:15.09--h2d50403_4' }"
input:
tuple val(meta), path(archive)
output:
tuple val(meta), path("${archive.baseName}/"), emit: unzipped_archive
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
if ( archive instanceof List && archive.name.size > 1 ) { exit 1, "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." }
"""
7za \\
e \\
-o"${archive.baseName}"/ \\
$args \\
$archive
cat <<-END_VERSIONS > versions.yml
"${task.process}":
7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
END_VERSIONS
"""
}