process PYDAMAGE_ANALYZE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::pydamage=0.70" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' : 'quay.io/biocontainers/pydamage:0.70--pyhdfd78af_0' }" input: tuple val(meta), path(bam), path(bai) output: tuple val(meta), path("pydamage_results/pydamage_results.csv"), emit: csv 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}" """ pydamage \\ analyze \\ $args \\ -p $task.cpus \\ $bam cat <<-END_VERSIONS > versions.yml "${task.process}": pydamage: \$(echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g') END_VERSIONS """ }