mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
eff515891d
* new module fargene * Update main.nf * Update modules/fargene/main.nf * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
63 lines
3.4 KiB
Text
63 lines
3.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
def VERSION = '0.1'
|
|
|
|
process FARGENE {
|
|
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::fargene=0.1" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4"
|
|
} else {
|
|
container "quay.io/biocontainers/fargene:0.1--py27h21c881e_4"
|
|
}
|
|
|
|
input:
|
|
// input may be fasta (for genomes or longer contigs) or paired-end fastq (for metagenome), the latter in addition with --meta flag
|
|
tuple val(meta), path(input)
|
|
val hmm_model
|
|
|
|
output:
|
|
path "*.log" , emit: log
|
|
path "${prefix}/results_summary.txt" , emit: txt
|
|
tuple val(meta), path("${prefix}/hmmsearchresults/*.out") , optional: true, emit: hmm
|
|
tuple val(meta), path("${prefix}/predictedGenes/predicted-orfs.fasta") , optional: true, emit: orfs
|
|
tuple val(meta), path("${prefix}/predictedGenes/predicted-orfs-amino.fasta") , optional: true, emit: orfs_amino
|
|
tuple val(meta), path("${prefix}/predictedGenes/retrieved-contigs.fasta") , optional: true, emit: contigs
|
|
tuple val(meta), path("${prefix}/predictedGenes/retrieved-contigs-peptides.fasta") , optional: true, emit: contigs_pept
|
|
tuple val(meta), path("${prefix}/predictedGenes/*filtered.fasta") , optional: true, emit: filtered
|
|
tuple val(meta), path("${prefix}/predictedGenes/*filtered-peptides.fasta") , optional: true, emit: filtered_pept
|
|
tuple val(meta), path("${prefix}/retrievedFragments/all_retrieved_*.fastq") , optional: true, emit: fragments
|
|
tuple val(meta), path("${prefix}/retrievedFragments/retrievedFragments/trimmedReads/*.fasta"), optional: true, emit: trimmed
|
|
tuple val(meta), path("${prefix}/spades_assembly/*") , optional: true, emit: spades
|
|
tuple val(meta), path("${prefix}/tmpdir/*.fasta") , optional: true, emit: metagenome
|
|
tuple val(meta), path("${prefix}/tmpdir/*.out") , optional: true, emit: tmp
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
gzip \\
|
|
-cdf $input \\
|
|
> unziped.fa |
|
|
fargene \\
|
|
$options.args \\
|
|
-p $task.cpus \\
|
|
-i unziped.fa \\
|
|
--hmm-model $hmm_model \\
|
|
-o $prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo $VERSION)
|
|
END_VERSIONS
|
|
"""
|
|
}
|