process PAIRTOOLS_SELECT { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null) container "${ 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(input) output: tuple val(meta), path("*.selected.pairs.gz") , emit: selected tuple val(meta), path("*.unselected.pairs.gz"), emit: unselected path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" """ pairtools select \\ "$args" \\ -o ${prefix}.selected.pairs.gz \\ --output-rest ${prefix}.unselected.pairs.gz \\ ${input} cat <<-END_VERSIONS > versions.yml "${task.process}": pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //') END_VERSIONS """ }