process RSEQC_READDUPLICATION { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' : 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("*seq.DupRate.xls"), emit: seq_xls tuple val(meta), path("*pos.DupRate.xls"), emit: pos_xls tuple val(meta), path("*.pdf") , emit: pdf tuple val(meta), path("*.r") , emit: rscript path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ read_duplication.py \\ -i $bam \\ -o $prefix \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": rseqc: \$(read_duplication.py --version | sed -e "s/read_duplication.py //g") END_VERSIONS """ }