kkonganti@11: process PROKKA {
kkonganti@11:     tag "$meta.id"
kkonganti@11:     label 'process_low'
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${params.swmodulepath}${params.fs}prokka${params.fs}1.14.5" : null)
kkonganti@11:     conda (params.enable_conda ? "bioconda::prokka=1.14.6 conda-forge::perl" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl5321hdfd78af_4' :
kkonganti@11:         'quay.io/biocontainers/prokka:1.14.6--pl5321hdfd78af_4' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         tuple val(meta), path(fasta), path(proteins), path(prodigal_tf)
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         tuple val(meta), path("${prefix}/*.gff"), emit: gff
kkonganti@11:         tuple val(meta), path("${prefix}/*.gbk"), emit: gbk
kkonganti@11:         tuple val(meta), path("${prefix}/*.fna"), emit: fna
kkonganti@11:         tuple val(meta), path("${prefix}/*.faa"), emit: faa
kkonganti@11:         tuple val(meta), path("${prefix}/*.ffn"), emit: ffn
kkonganti@11:         tuple val(meta), path("${prefix}/*.sqn"), emit: sqn
kkonganti@11:         tuple val(meta), path("${prefix}/*.fsa"), emit: fsa
kkonganti@11:         tuple val(meta), path("${prefix}/*.tbl"), emit: tbl
kkonganti@11:         tuple val(meta), path("${prefix}/*.err"), emit: err
kkonganti@11:         tuple val(meta), path("${prefix}/*.log"), emit: log
kkonganti@11:         tuple val(meta), path("${prefix}/*.txt"), emit: txt
kkonganti@11:         tuple val(meta), path("${prefix}/*.tsv"), emit: tsv
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 proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
kkonganti@11:         def prodigal_tf  = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : ""
kkonganti@11:         def prefix_l     = "${meta.id}" ?: ''
kkonganti@11:         prefix           = task.ext.prefix ?: "${meta.id}"
kkonganti@11:         def strain       = !params.prokka_strain && prefix_l ? "--strain '${prefix_l}'" : ''
kkonganti@11: 
kkonganti@11:         """
kkonganti@11:         prokka \\
kkonganti@11:             $strain \\
kkonganti@11:             $args \\
kkonganti@11:             --cpus $task.cpus \\
kkonganti@11:             --prefix $prefix \\
kkonganti@11:             $proteins_opt \\
kkonganti@11:             $prodigal_tf \\
kkonganti@11:             $fasta
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             prokka: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //')
kkonganti@11:         END_VERSIONS
kkonganti@11:         """
kkonganti@11: }