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409af2f27c
* feat: code polishing * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * code polishing * more code polishing * code polishing * tests for applybqsrspark * fix typo * no need to check md5sum for versions.yml * fix: use correct syntax * code polishing again * add tests for markduplicatesspark * simplify mergevcfs tests * add tests for baserecalibratorspark * fix: path to entry * code polishing * fix linting * simplify module * update meta.yml * fix pair mode * fix: MITO mode * more tests * fix command * bad copy paste * fix typos * fix tests * fix test * update meta.yml * correct versions.yml in all test.yml * code polishing * code polishing * more code polishing * fix args * add tmpdir for all Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
67 lines
2.5 KiB
Text
67 lines
2.5 KiB
Text
process GATK4_GENOMICSDBIMPORT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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input:
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tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace)
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val run_intlist
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val run_updatewspace
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val input_map
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output:
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tuple val(meta), path("$prefix") , optional:true, emit: genomicsdb
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tuple val(meta), path("$updated_db") , optional:true, emit: updatedb
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tuple val(meta), path("*.interval_list"), optional:true, emit: intervallist
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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// settings for running default create gendb mode
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input_command = input_map ? "--sample-name-map ${vcf[0]}" : vcf.collect(){"--variant $it"}.join(' ')
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genomicsdb_command = "--genomicsdb-workspace-path ${prefix}"
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interval_command = interval_file ? "--intervals ${interval_file}" : "--intervals ${interval_value}"
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// settings changed for running get intervals list mode if run_intlist is true
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if (run_intlist) {
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genomicsdb_command = "--genomicsdb-update-workspace-path ${wspace}"
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interval_command = "--output-interval-list-to-file ${prefix}.interval_list"
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}
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// settings changed for running update gendb mode. input_command same as default, update_db forces module to emit the updated gendb
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if (run_updatewspace) {
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genomicsdb_command = "--genomicsdb-update-workspace-path ${wspace}"
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interval_command = ''
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updated_db = "${wspace}"
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}
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK GenomicsDBImport] 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 --java-options "-Xmx${avail_mem}g" GenomicsDBImport \\
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$input_command \\
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$genomicsdb_command \\
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$interval_command \\
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--tmp-dir . \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(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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