kkonganti@11: process PRODIGAL {
kkonganti@11:     tag "$meta.id"
kkonganti@11:     label 'process_nano'
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${params.swmodulepath}${params.fs}prodigal${params.fs}2.6.3" : null)
kkonganti@11:     conda (params.enable_conda ? "bioconda::prodigal=2.6.3 conda-forge::pigz=2.6" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' :
kkonganti@11:         'quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         tuple val(meta), path(genome)
kkonganti@11:         val(output_format)
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         tuple val(meta), path("*.${output_format}"), emit: gene_annotations
kkonganti@11:         tuple val(meta), path("*.fna")             , emit: cds
kkonganti@11:         tuple val(meta), path("*.faa")             , emit: proteins
kkonganti@11:         tuple val(meta), path("*_all.txt")         , emit: all_gene_annotations
kkonganti@11:         tuple val(meta), path("*trn")              , emit: trained, optional: true
kkonganti@11:         path "versions.yml"                        , emit: versions
kkonganti@11: 
kkonganti@11:     when:
kkonganti@11:         task.ext.when == null || task.ext.when
kkonganti@11: 
kkonganti@11:     script:
kkonganti@11:         def args          = task.ext.args   ?: ''
kkonganti@11:         def prefix        = task.ext.prefix ?: "${meta.id}"
kkonganti@11:         def training      = args.toString().matches(/.*-t/) ? "-t ${prefix}.trn" : ''
kkonganti@11:         args              = args.toString().replace(/-t/, '')
kkonganti@11:         """
kkonganti@11:         if [ "$training" = "-t ${prefix}.trn" ]; then
kkonganti@11:             touch "${prefix}.fna"
kkonganti@11:             touch "${prefix}.faa"
kkonganti@11:             touch "${prefix}_all.txt"
kkonganti@11:             touch "${prefix}.${output_format}"
kkonganti@11: 
kkonganti@11:             prodigal \\
kkonganti@11:                 $training \\
kkonganti@11:                 -i $genome
kkonganti@11:         fi
kkonganti@11: 
kkonganti@11:         prodigal \\
kkonganti@11:             $args \\
kkonganti@11:             -d "${prefix}.fna" \\
kkonganti@11:             -o "${prefix}.${output_format}" \\
kkonganti@11:             -a "${prefix}.faa" \\
kkonganti@11:             -s "${prefix}_all.txt" \\
kkonganti@11:             -i $genome
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
kkonganti@11:         END_VERSIONS
kkonganti@11:         """
kkonganti@11: }