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https://github.com/MillironX/nf-core_modules.git
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572abb00b3
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
48 lines
1.5 KiB
Text
48 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_MERGEVCFS {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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:meta.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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tuple val(meta), path(vcfs)
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path(ref_dict)
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val use_ref_dict
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output:
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tuple val(meta), path('*.vcf.gz') , emit: vcf
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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 prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
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// Make list of VCFs to merge
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def input = ""
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for (vcf in vcfs) {
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input += " I=${vcf}"
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}
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def ref = use_ref_dict ? "D=${ref_dict}" : ""
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"""
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gatk MergeVcfs \\
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$input \\
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O=${prefix}.merged.vcf.gz \\
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$ref \\
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$options.args
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gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
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"""
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}
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