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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
22 lines
764 B
Text
22 lines
764 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_FASTQTOSAM } from '../../../../modules/gatk4/fastqtosam/main.nf' addParams( options: [:] )
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workflow test_gatk4_fastqtosam_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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GATK4_FASTQTOSAM ( input )
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}
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workflow test_gatk4_fastqtosam_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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GATK4_FASTQTOSAM ( input )
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}
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