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 script: def args = task.ext.args ?: '' def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${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 """ }