nf-core_modules/software/prokka/main.nf

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