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45 lines
1.5 KiB
Text
45 lines
1.5 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 GATK4_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), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--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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def avail_mem = 6
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if (!task.memory) {
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log.info '[GATK] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" \\
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CreateSequenceDictionary \\
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--REFERENCE $fasta \\
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--URI $fasta \\
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$options.args
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echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt
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"""
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}
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