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https://github.com/MillironX/nf-core_modules.git
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6ff995e93d
* initial commit [ci skip] * add basic structure [ci skip] * finalized the bcftools/query module * add optional files [ci skip] * Add the vcf index file as param [ci skip] * update the md5sum for output file [ci skip] * all tests passing
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_QUERY } from '../../../../modules/bcftools/query/main.nf' addParams( options: ['args': "-f '%CHROM %POS %REF %ALT[%SAMPLE=%GT]'" ] )
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workflow test_bcftools_query {
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regions = []
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targets = []
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samples = []
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input = [ [ id:'out' ], // 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_QUERY ( input, regions, targets, samples )
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}
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workflow test_bcftools_query_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' ], // 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_QUERY ( input, regions, targets, samples )
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}
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