process PAIRTOOLS_PARSE { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' : 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }" input: tuple val(meta), path(bam) path chromsizes output: tuple val(meta), path("*.pairsam.gz") , emit: pairsam tuple val(meta), path("*.pairsam.stat"), emit: stat 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}" """ pairtools \\ parse \\ -c $chromsizes \\ $args \\ --output-stats ${prefix}.pairsam.stat \\ -o ${prefix}.pairsam.gz \\ $bam cat <<-END_VERSIONS > versions.yml "${task.process}": pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //') END_VERSIONS """ }