nf-core_modules/modules/gunzip/main.nf
James A. Fellows Yates 90aef30f43
Set process label to process_single for modules with no task.cpus usage (#2076)
* Set process label to `process_single` for modules with no `task.cpus` usage

* Fix tests of 'borked' modules

* prettier

* More modules are single-threaded and can use process_single

* Adding process_single to hmmer/esl* modules

* Fix failing tests

* Prettier

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2022-09-19 11:54:47 +02:00

44 lines
1.1 KiB
Text

process GUNZIP {
tag "$archive"
label 'process_single'
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ 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("$gunzip"), emit: gunzip
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
gunzip = archive.toString() - '.gz'
"""
gunzip \\
-f \\
$args \\
$archive
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
END_VERSIONS
"""
stub:
gunzip = archive.toString() - '.gz'
"""
touch $gunzip
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
END_VERSIONS
"""
}