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* 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
26 lines
1 KiB
Text
26 lines
1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_MERGEVCFS } from '../../../../modules/gatk4/mergevcfs/main.nf' addParams( options: [:] )
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workflow test_gatk4_mergevcfs {
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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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file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
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]
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MERGEVCFS ( input, dict, false )
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}
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workflow test_gatk4_mergevcfs_refdict {
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def input = []
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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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file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
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]
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_MERGEVCFS ( input, dict, true )
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}
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