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https://github.com/MillironX/nf-core_modules.git
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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
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process ARTIC_GUPPYPLEX {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::artic=1.2.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0"
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} else {
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container "quay.io/biocontainers/artic:1.2.1--py_0"
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}
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input:
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tuple val(meta), path(fastq_dir)
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output:
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tuple val(meta), path("*.fastq.gz"), emit: fastq
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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artic \\
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guppyplex \\
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$options.args \\
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--directory $fastq_dir \\
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--output ${prefix}.fastq
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pigz -p $task.cpus *.fastq
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echo \$(artic --version 2>&1) | sed 's/^.*artic //; s/ .*\$//' > ${software}.version.txt
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"""
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}
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