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c5634ba99b
* initial commit [ci skip] * add stubs [ci skip] * Finalize the bcftools/view module * accomodate optional files * add optional region file * refer the targets file in the tests * all tests passing * documen the optional parameters
31 lines
1.1 KiB
Text
31 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BCFTOOLS_VIEW } from '../../../../modules/bcftools/view/main.nf' addParams( options: ['args': '--no-version'] )
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workflow test_bcftools_view {
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regions = []
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targets = []
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samples = []
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input = [[ id:'out', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
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BCFTOOLS_VIEW ( input, regions, targets, samples )
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}
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workflow test_bcftools_view_with_optional_files {
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regions = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
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targets = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
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samples = []
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input = [[ id:'out', single_end:false ], // 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']['test2_vcf_gz_tbi'], checkIfExists: true)]
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BCFTOOLS_VIEW ( input, regions, targets, samples )
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}
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