nf-core_modules/modules/prodigal/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PRODIGAL {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::prodigal=2.6.3" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/prodigal:2.6.3--h516909a_2"
} else {
container "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("${prefix}_all.txt"), emit: all_gene_annotations
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
prodigal -i "${genome}" \\
$options.args \\
-f $output_format \\
-d "${prefix}.fna" \\
-o "${prefix}.${output_format}" \\
-a "${prefix}.faa" \\
-s "${prefix}_all.txt"
echo \$(prodigal -v 2>&1) | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p' > ${software}.version.txt
"""
}