mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
daab0a77dd
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Update main.nf * Remove now unnecessary input channel * Remove unused channel from tests * Update hAMRonization to 1.1.1 and add hAMRonization farGene * Fix hamronizatio ntests * Prettier * Fix fargene linting * Correct file * Fix fargene output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * Fix summarise tests * Prettier Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
53 lines
3.1 KiB
Text
53 lines
3.1 KiB
Text
process FARGENE {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
|
conda (params.enable_conda ? "bioconda::fargene=0.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4' :
|
|
'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:
|
|
tuple val(meta), path("*.log") , emit: log
|
|
tuple val(meta), 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("${prefix}/tmpdir/*.out") , optional: true, emit: tmp
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
prefix = task.ext.prefix ?: "${meta.id}"
|
|
def VERSION = '0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
"""
|
|
fargene \\
|
|
$args \\
|
|
-p $task.cpus \\
|
|
-i $input \\
|
|
--hmm-model $hmm_model \\
|
|
-o $prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
fargene: $VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|