process PRODIGAL { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::prodigal=2.6.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/prodigal:2.6.3--h516909a_2' : 'quay.io/biocontainers/prodigal:2.6.3--h516909a_2' }" input: tuple val(meta), path(genome) val(output_format) output: tuple val(meta), path("${prefix}.${output_format}"), emit: gene_annotations tuple val(meta), path("${prefix}.fna"), emit: nucleotide_fasta tuple val(meta), path("${prefix}.faa"), emit: amino_acid_fasta tuple val(meta), path("${prefix}_all.txt"), emit: all_gene_annotations path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" """ prodigal -i "${genome}" \\ $args \\ -f $output_format \\ -d "${prefix}.fna" \\ -o "${prefix}.${output_format}" \\ -a "${prefix}.faa" \\ -s "${prefix}_all.txt" cat <<-END_VERSIONS > versions.yml "${task.process}": prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p') END_VERSIONS """ }