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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
9 lines
308 B
Text
9 lines
308 B
Text
process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: 'GATK4_LEFTALIGNANDTRIMVARIANTS' {
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ext.args = "--split-multi-allelics --dont-trim-alleles --keep-original-ac"
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ext.prefix = { "${meta.id}.normalised" }
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}
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}
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