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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
40 lines
1.4 KiB
Text
40 lines
1.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { VCFTOOLS as VCFTOOLS_BASE } from '../../../modules/vcftools/main.nf' addParams( options: ['args': '--freq'] )
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include { VCFTOOLS as VCFTOOLS_OPTIONAL } from '../../../modules/vcftools/main.nf' addParams( options: ['args': '--freq --exclude-bed'] )
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workflow test_vcftools_vcf_base {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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]
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VCFTOOLS_BASE ( input, [], [] )
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}
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workflow test_vcftools_vcfgz_base {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
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]
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VCFTOOLS_BASE ( input, [], [] )
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}
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workflow test_vcftools_vcf_optional {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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]
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bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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VCFTOOLS_OPTIONAL ( input, bed, [] )
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}
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workflow test_vcftools_vcfgz_optional {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
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]
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bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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VCFTOOLS_OPTIONAL ( input, bed, [] )
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}
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