nf-core_modules/software/last/mafswap/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process LAST_MAFSWAP {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::last=1219" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0"
} else {
container "quay.io/biocontainers/last:1219--h2e03b76_0"
}
input:
tuple val(meta), path(maf)
output:
tuple val(meta), path("*.maf.gz"), emit: maf
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
zcat $maf | maf-swap $options.args | gzip --no-name > ${prefix}.swapped.maf.gz
# maf-swap has no --version option but lastdb, part of the same package, has.
echo \$(lastdb --version 2>&1) | sed 's/lastdb //' > ${software}.version.txt
"""
}