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39 lines
1.3 KiB
Text
39 lines
1.3 KiB
Text
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// 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 GATK_CREATESEQUENCEDICTIONARY {
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tag "$fasta"
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label 'process_medium'
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publishDir "${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), publish_id:'') }
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conda (params.enable_conda ? "bioconda::gatk4=4.1.9.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.1.9.0--py39_0"
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}
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input:
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path fasta
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output:
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path "*.dict" , emit: dict
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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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"""
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gatk --java-options "-Xmx${task.memory.toGiga()}g" \\
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CreateSequenceDictionary \\
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--REFERENCE $fasta \\
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$options.args
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echo \$(gatk CreateSequenceDictionary --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt
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"""
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}
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