mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
dce27b8102
* Update functions.nf * Replace saveAs line in module main script * Add spacing for ECLint
52 lines
1.9 KiB
Text
52 lines
1.9 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
def options = initOptions(params.options)
|
|
|
|
process KRAKEN2_RUN {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
publishDir "${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::kraken2=2.1.1' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container 'https://depot.galaxyproject.org/singularity/kraken2:2.1.1--pl526hc9558a2_0'
|
|
} else {
|
|
container 'quay.io/biocontainers/kraken2:2.1.1--pl526hc9558a2_0'
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
path db
|
|
|
|
output:
|
|
tuple val(meta), path('*classified*') , emit: classified
|
|
tuple val(meta), path('*unclassified*'), emit: unclassified
|
|
tuple val(meta), path('*report.txt') , emit: txt
|
|
path '*.version.txt' , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def paired = meta.single_end ? "" : "--paired"
|
|
def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq"
|
|
def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
|
|
"""
|
|
kraken2 \\
|
|
--db $db \\
|
|
--threads $task.cpus \\
|
|
--unclassified-out $unclassified \\
|
|
--classified-out $classified \\
|
|
--report ${prefix}.kraken2.report.txt \\
|
|
--gzip-compressed \\
|
|
$paired \\
|
|
$options.args \\
|
|
$reads
|
|
|
|
gzip *.fastq
|
|
echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|