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009f7c691c
* Added: gatk4/leftalignandtrimvariants Additions: - GATK4/LeftAlignAndTrimVariants module - Use sars-ncov2 test data as this normalises a larger INDEL correctly. Fixes #1801 * fixup: Added index to output spec * fixup: Pattern of tbi output corrected to 'tbi' * gatk4/leftalignandtrimvariants: Added intervals Changes: - gatk4/leftalignandtrimvariants now supports optional interval as BED file - Tests added with and without interval. Not test BED file excludes all variants so no variants are actually normalised. Fixes #1801 * fixup: leftalignandtrimvariants vcf->tbi fix * fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml
48 lines
1.6 KiB
Text
48 lines
1.6 KiB
Text
process GATK4_LEFTALIGNANDTRIMVARIANTS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(vcf), path(tbi), path(intervals)
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path fasta
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path fai
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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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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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def prefix = task.ext.prefix ?: "${meta.id}"
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def interval_command = intervals ? "--intervals $intervals" : ""
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK LeftAlignAndTrimVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.toGiga()
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}
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"""
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gatk --java-options "-Xmx${avail_mem}G" LeftAlignAndTrimVariants \\
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$interval_command \\
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--variant $vcf \\
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--output ${prefix}.vcf.gz \\
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--reference $fasta \\
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--tmp-dir . \\
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$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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