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79a9d5e1ea
NGSCheckMate ncm mode, working on bam files and vcf files to check that (human) samples match as expected Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
27 lines
No EOL
611 B
Text
27 lines
No EOL
611 B
Text
process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: BEDTOOLS_MAKEWINDOWS {
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ext.args = '-w 1'
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}
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withName: BCFTOOLS_MPILEUP {
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ext.args2 = '--no-version --ploidy 1 --multiallelic-caller'
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ext.args3 = '--no-version'
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}
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withName: BCFTOOLS_MPILEUP2 {
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ext.args2 = '--no-version --ploidy 1 --multiallelic-caller'
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ext.args3 = '--no-version'
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}
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withName: NGSCHECKMATE_NCM_VCF {
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ext.args = '-V'
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}
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withName: NGSCHECKMATE_NCM_BAM {
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ext.args = '-B'
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}
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} |