process PIRATE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::pirate=1.0.4" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pirate%3A1.0.4--hdfd78af_1' : 'quay.io/biocontainers/pirate:1.0.4--hdfd78af_1' }" input: tuple val(meta), path(gff) output: tuple val(meta), path("results/*") , emit: results tuple val(meta), path("results/core_alignment.fasta"), optional: true, emit: aln path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ PIRATE \\ $args \\ --threads $task.cpus \\ --input ./ \\ --output results/ cat <<-END_VERSIONS > versions.yml "${task.process}": pirate: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' ) END_VERSIONS """ }