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56 lines
2.1 KiB
Text
56 lines
2.1 KiB
Text
include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process PROKKA {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl526_0"
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} else {
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container "quay.io/biocontainers/prokka:1.14.6--pl526_0"
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}
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input:
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tuple val(meta), path(fasta)
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path proteins
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path prodigal_tf
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output:
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tuple val(meta), path("${prefix}/*.gff"), emit: gff
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tuple val(meta), path("${prefix}/*.gbk"), emit: gbk
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tuple val(meta), path("${prefix}/*.fna"), emit: fna
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tuple val(meta), path("${prefix}/*.faa"), emit: faa
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tuple val(meta), path("${prefix}/*.ffn"), emit: ffn
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tuple val(meta), path("${prefix}/*.sqn"), emit: sqn
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tuple val(meta), path("${prefix}/*.fsa"), emit: fsa
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tuple val(meta), path("${prefix}/*.tbl"), emit: tbl
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tuple val(meta), path("${prefix}/*.err"), emit: err
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tuple val(meta), path("${prefix}/*.log"), emit: log
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tuple val(meta), path("${prefix}/*.txt"), emit: txt
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tuple val(meta), path("${prefix}/*.tsv"), emit: tsv
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
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def prodigal_opt = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : ""
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"""
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prokka \\
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$options.args \\
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--cpus $task.cpus \\
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--prefix $prefix \\
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$proteins_opt \\
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$prodigal_tf \\
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$fasta
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echo \$(prokka --version 2>&1) | sed 's/^.*prokka //' > ${software}.version.txt
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"""
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}
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