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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
18 lines
850 B
Text
18 lines
850 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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test_options = ['args': '--filter-name "test_filter" --filter-expression "MQ0 > 0"', 'suffix': '.filtered']
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include { GATK4_VARIANTFILTRATION } from '../../../../modules/gatk4/variantfiltration/main.nf' addParams( options: test_options )
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workflow test_gatk4_variantfiltration {
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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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fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
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fai = [ file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
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genome_dict = [ file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
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GATK4_VARIANTFILTRATION ( input, fasta, fai, genome_dict )
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}
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