process MTNUCRATIO { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mtnucratio:0.7--hdfd78af_2' : 'quay.io/biocontainers/mtnucratio:0.7--hdfd78af_2' }" input: tuple val(meta), path(bam) val(mt_id) output: tuple val(meta), path("*.mtnucratio"), emit: mtnucratio tuple val(meta), path("*.json") , emit: json 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}" """ mtnucratio \\ $args \\ $bam \\ $mt_id cat <<-END_VERSIONS > versions.yml "${task.process}": mtnucratio: \$(echo \$(mtnucratio --version 2>&1) | head -n1 | sed 's/Version: //') END_VERSIONS """ }