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889465cb2b
* update test data paths * Update test md5sums * gatk test fixes & update variantfiltration main * few extra fixes after review * fix suspected format error * Update software/gatk4/variantfiltration/main.nf * Update software/gatk4/variantfiltration/main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
17 lines
798 B
Text
17 lines
798 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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//keep --no-verson argument, otherwise md5 will change on each execution
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include { BCFTOOLS_MERGE } from '../../../../software/bcftools/merge/main.nf' addParams( options: ['args': '--force-samples --no-version'] )
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workflow test_bcftools_merge {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) ]
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]
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BCFTOOLS_MERGE ( input )
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}
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