process LAST_MAFCONVERT { tag "$meta.id" label 'process_high' conda (params.enable_conda ? 'bioconda::last=1250' : null) container "${ 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) val(format) output: tuple val(meta), path("*.axt.gz"), optional:true, emit: axt_gz tuple val(meta), path("*.blast.gz"), optional:true, emit: blast_gz tuple val(meta), path("*.blasttab.gz"), optional:true, emit: blasttab_gz tuple val(meta), path("*.chain.gz"), optional:true, emit: chain_gz tuple val(meta), path("*.gff.gz"), optional:true, emit: gff_gz tuple val(meta), path("*.html.gz"), optional:true, emit: html_gz tuple val(meta), path("*.psl.gz"), optional:true, emit: psl_gz tuple val(meta), path("*.sam.gz"), optional:true, emit: sam_gz tuple val(meta), path("*.tab.gz"), optional:true, emit: tab_gz 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-convert $args $format $maf | gzip --no-name \\ > ${prefix}.${format}.gz # maf-convert 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 """ }