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3b600af50e
* feat: update gatk4 from 4.2.0.0 to 4.2.3.0 * update md5checksum * commit all files * actually checksum was good, but I suspect something fishy with the tests
59 lines
2 KiB
Text
59 lines
2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process GATK4_BASERECALIBRATOR {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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tuple val(meta), path(input), path(input_index)
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path fasta
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path fastaidx
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path dict
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path intervalsBed
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path knownSites
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path knownSites_tbi
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output:
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tuple val(meta), path("*.table"), emit: table
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
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def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')
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if (!task.memory) {
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log.info '[GATK BaseRecalibrator] Available memory not known - defaulting to 3GB. 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 BaseRecalibrator \
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-R $fasta \
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-I $input \
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$sitesCommand \
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$intervalsCommand \
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--tmp-dir . \
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$options.args \
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-O ${prefix}.table
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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