mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 00:02:04 +00:00
d63ff4ba1b
* Adding artic guppyplex module * Adding guppyplex tests * Fix tests * Correcting typo * Fix lint * Fix test * Missing description * Missing descriptions * Update functions to last version as suggested * Bump newest version of nanoplot
41 lines
1.4 KiB
Text
41 lines
1.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process ARTIC_GUPPYPLEX {
|
|
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::artic=1.2.1" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0"
|
|
} else {
|
|
container "quay.io/biocontainers/artic:1.2.1--py_0"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(fastq_dir)
|
|
|
|
output:
|
|
tuple val(meta), path("*.fastq.gz"), emit: fastq
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
artic \\
|
|
guppyplex \\
|
|
$options.args \\
|
|
--directory $fastq_dir \\
|
|
--output ${prefix}.fastq
|
|
|
|
pigz -p $task.cpus *.fastq
|
|
echo \$(artic --version 2>&1) | sed 's/^.*artic //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|