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https://github.com/MillironX/nf-core_modules.git
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86bb832fae
* nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
54 lines
2.1 KiB
Text
54 lines
2.1 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 STRELKA_GERMLINE {
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tag "$meta.id"
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label 'process_high'
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publishDir "${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::strelka=2.9.10" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--0"
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} else {
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container "quay.io/biocontainers/strelka:2.9.10--0"
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}
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input:
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tuple val(meta), path(bam), path(bai)
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path fasta
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path fai
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path target_bed
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output:
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tuple val(meta), path("*_variants.vcf.gz"), emit: vcf
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tuple val(meta), path("*_variants.vcf.gz.tbi"), emit: vcf_tbi
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tuple val(meta), path("*_genome.vcf.gz"), emit: genome_vcf
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tuple val(meta), path("*_genome.vcf.gz.tbi"), emit: genome_vcf_tbi
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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 ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "strelka_${meta.id}${ioptions.suffix}" : "strelka_${meta.id}"
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options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
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"""
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configureStrelkaGermlineWorkflow.py \
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--bam ${bam} \
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--referenceFasta ${fasta} \
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${options_strelka} \
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${options.args} \
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--runDir strelka
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python strelka/runWorkflow.py -m local -j ${task.cpus}
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mv strelka/results/variants/genome.*.vcf.gz ${prefix}_genome.vcf.gz
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mv strelka/results/variants/genome.*.vcf.gz.tbi ${prefix}_genome.vcf.gz.tbi
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mv strelka/results/variants/variants.vcf.gz ${prefix}_variants.vcf.gz
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mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}_variants.vcf.gz.tbi
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echo configureStrelkaGermlineWorkflow.py --version &> ${software}.version.txt #2>&1
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"""
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}
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