process UMITOOLS_EXTRACT { tag "$meta.id" label "process_low" conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null) container "${ 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(reads) output: tuple val(meta), path("*.fastq.gz"), emit: reads tuple val(meta), path("*.log") , emit: log path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ umi_tools \\ extract \\ -I $reads \\ -S ${prefix}.umi_extract.fastq.gz \\ $args \\ > ${prefix}.umi_extract.log cat <<-END_VERSIONS > versions.yml "${task.process}": umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') END_VERSIONS """ } else { """ umi_tools \\ extract \\ -I ${reads[0]} \\ --read2-in=${reads[1]} \\ -S ${prefix}.umi_extract_1.fastq.gz \\ --read2-out=${prefix}.umi_extract_2.fastq.gz \\ $args \\ > ${prefix}.umi_extract.log cat <<-END_VERSIONS > versions.yml "${task.process}": umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//') END_VERSIONS """ } }