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3c8ca3fec4
* files created for createsompon, script written, meta written, still needs tests * updated to 2.0.0 method input, however this requires a genomicsDB input now * script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests * versions updated, issue with test data not able to download directory * updated tests to include repo-side data * Apply suggestions from code review * Update modules/gatk4/createsomaticpanelofnormals/main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
47 lines
1.5 KiB
Text
47 lines
1.5 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_CREATESOMATICPANELOFNORMALS {
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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=4.2.0.0" : 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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tuple val(meta), path(genomicsdb)
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path fasta
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path fastaidx
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path dict
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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tuple val(meta), path("*.tbi") , emit: tbi
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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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"""
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gatk \\
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CreateSomaticPanelOfNormals \\
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-R $fasta \\
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-V gendb://$genomicsdb \\
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-O ${prefix}.vcf.gz \\
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$options.args
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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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