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c99ab09f8d
* Add kraken2 pigz multi-tool container for compressing output fastq files * Add untar to pytest config * Add untar process to kraken2 tests * Remove unneeded tags
53 lines
2.1 KiB
Text
53 lines
2.1 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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def options = initOptions(params.options)
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process KRAKEN2_RUN {
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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::kraken2=2.1.1 conda-forge::pigz=2.6' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0'
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} else {
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container 'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0'
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}
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input:
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tuple val(meta), path(reads)
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path db
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output:
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tuple val(meta), path('*classified*') , emit: classified
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tuple val(meta), path('*unclassified*'), emit: unclassified
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tuple val(meta), path('*report.txt') , emit: txt
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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}" : "${meta.id}"
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def paired = meta.single_end ? "" : "--paired"
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def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq"
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def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
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"""
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kraken2 \\
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--db $db \\
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--threads $task.cpus \\
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--unclassified-out $unclassified \\
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--classified-out $classified \\
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--report ${prefix}.kraken2.report.txt \\
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--gzip-compressed \\
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$paired \\
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$options.args \\
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$reads
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pigz -p $task.cpus *.fastq
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echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//' > ${software}.version.txt
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"""
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}
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