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https://github.com/MillironX/nf-core_modules.git
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50eafb19c6
* Update version for log4j vulnerability * update checksums * update checksums * update checksums * Remove todo string * remove werid output paths * remove werid output paths * remove werid output paths * Update various checksums * Update various checksums * Remove unstable md5sums * Update md5sums * Fix pileupsummary * Fix genotypegvcfs * Update test files mutect2 * hm genotypevcf updated again * Update some mutect checksums and whatnot * Fix last mutect checksum * Apply suggestion to use mtochondria data instead
55 lines
1.8 KiB
Text
55 lines
1.8 KiB
Text
process GATK4_APPLYVQSR {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
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input:
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tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches)
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path fasta
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path fai
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path dict
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val allelespecific
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val truthsensitivity
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val mode
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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 args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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refCommand = fasta ? "-R ${fasta} " : ''
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alleleSpecificCommand = allelespecific ? '-AS' : ''
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truthSensitivityCommand = truthsensitivity ? "--truth-sensitivity-filter-level ${truthsensitivity}" : ''
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modeCommand = mode ? "--mode ${mode} " : 'SNP'
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK ApplyVQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" ApplyVQSR \\
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${refCommand} \\
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-V ${vcf} \\
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-O ${prefix}.vcf.gz \\
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${alleleSpecificCommand} \\
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${truthSensitivityCommand} \\
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--tranches-file $tranches \\
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--recal-file $recal \\
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${modeCommand} \\
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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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