process PRESEQ_LCEXTRAP { tag "$meta.id" label 'process_medium' label 'error_ignore' conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h06ef8b0_1' : 'quay.io/biocontainers/preseq:3.1.2--h06ef8b0_1' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("*.ccurve.txt"), emit: ccurve tuple val(meta), path("*.log") , emit: log 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_end = meta.single_end ? '' : '-pe' """ preseq \\ lc_extrap \\ $args \\ $paired_end \\ -output ${prefix}.ccurve.txt \\ $bam cp .command.err ${prefix}.command.log cat <<-END_VERSIONS > versions.yml "${task.process}": preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//') END_VERSIONS """ }