nf-core_modules/modules/flash/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process FLASH {
tag "$meta.id"
label 'process_medium'
publishDir "${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::flash=1.2.11" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/flash:1.2.11--hed695b0_5"
} else {
container "quay.io/biocontainers/flash:1.2.11--hed695b0_5"
}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.merged.*.fastq.gz"), emit: reads
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def merged = "-o ${prefix}.merged"
def input_reads = "${reads[0]} ${reads[1]}"
"""
flash \\
$options.args \\
$merged \\
-z \\
$input_reads
echo \$(flash --version) > ${software}.version.txt
"""
}