mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
90aef30f43
* 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>
37 lines
1.4 KiB
Text
37 lines
1.4 KiB
Text
process ADAPTERREMOVALFIXPREFIX {
|
|
tag "$meta.id"
|
|
label 'process_single'
|
|
|
|
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
|
conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
|
|
'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"
|
|
|
|
input:
|
|
tuple val(meta), path(fastq)
|
|
|
|
output:
|
|
tuple val(meta), path("*.fq.gz"), emit: fixed_fastq
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
if ("$fastq" == "${prefix}.fq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
|
|
def VERSION = '0.0.5' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
"""
|
|
AdapterRemovalFixPrefix \\
|
|
$fastq \\
|
|
$args \\
|
|
| gzip > ${prefix}.fq.gz
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
adapterremovalfixprefix: $VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|