process DAMAGEPROFILER { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/damageprofiler:1.1--hdfd78af_2' : 'quay.io/biocontainers/damageprofiler:1.1--hdfd78af_2' }" input: tuple val(meta), path(bam) path fasta path fai path specieslist output: tuple val(meta), path("${prefix}"), emit: results path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "-r $fasta" : "" def species_list = specieslist ? "-sf $specieslist" : "" """ damageprofiler \\ -i $bam \\ -o $prefix/ \\ $args \\ $reference \\ $species_list cat <<-END_VERSIONS > versions.yml "${task.process}": damageprofiler: \$(damageprofiler -v | sed 's/^DamageProfiler v//') END_VERSIONS """ }