nf-core_modules/modules/last/mafswap/main.nf
2022-02-04 09:53:32 +01:00

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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
"""
}