nf-core_modules/modules/unzip/main.nf
James A. Fellows Yates e01a98a704
module: unzip (#642)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add unzip module

* Remove missing TODOs update mtea

* Apply changes after code-review from @grst

* Account for user trying to supply two input archives

* Remove debugging test

* Update modules/unzip/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Correct output path

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-08-02 09:40:57 +02:00

43 lines
1.4 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process UNZIP {
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 ? "bioconda::p7zip=15.09" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/p7zip:15.09--h2d50403_4"
} else {
container "quay.io/biocontainers/p7zip:15.09--h2d50403_4"
}
input:
path archive
output:
path "${archive.baseName}/" , emit: unzipped_archive
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
if ( archive instanceof List && archive.name.size > 1 ) { exit 1, "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." }
"""
7za \\
e \\
-o"${archive.baseName}"/ \\
$options.args \\
$archive
echo \$(7za --help) | grep Version | sed 's/.*p7zip Version//; s/(.*//' 1> ${software}.version.txt
"""
}