nf-core_modules/software/kraken2/run/main.nf

53 lines
1.9 KiB
Text
Raw Normal View History

// 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
"""
}