process UMITOOLS_DEDUP { tag "$meta.id" label "process_medium" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' : 'quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0' }" input: tuple val(meta), path(bam), path(bai) val get_output_stats output: tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*edit_distance.tsv"), optional:true, emit: tsv_edit_distance tuple val(meta), path("*per_umi.tsv") , optional:true, emit: tsv_per_umi tuple val(meta), path("*per_position.tsv") , optional:true, emit: tsv_umi_per_position 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}" def paired = meta.single_end ? "" : "--paired" def stats = get_output_stats ? "--output-stats $prefix" : "" if (!(args ==~ /.*--random-seed.*/)) {args += " --random-seed=100"} """ umi_tools \\ dedup \\ -I $bam \\ -S ${prefix}.bam \\ $stats \\ $paired \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') END_VERSIONS """ }