mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
32 lines
992 B
Text
32 lines
992 B
Text
process LAST_MAFSWAP {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? 'bioconda::last=1250' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
|
|
'quay.io/biocontainers/last:1250--h2e03b76_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(maf)
|
|
|
|
output:
|
|
tuple val(meta), path("*.maf.gz"), emit: maf
|
|
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}"
|
|
"""
|
|
maf-swap $args $maf | gzip --no-name > ${prefix}.swapped.maf.gz
|
|
|
|
# maf-swap has no --version option but lastdb, part of the same package, has.
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
last: \$(lastdb --version 2>&1 | sed 's/lastdb //')
|
|
END_VERSIONS
|
|
"""
|
|
}
|