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43 lines
1.2 KiB
Text
43 lines
1.2 KiB
Text
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nextflow.enable.dsl = 2
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include {
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TRIMMOMATIC as TRIMMOMATIC_SE
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TRIMMOMATIC as TRIMMOMATIC_PE
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TRIMMOMATIC
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} from '../../../modules/trimmomatic/main.nf'
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//
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// Test with single-end data
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//
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workflow test_trimmomatic_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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TRIMMOMATIC_SE ( input )
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}
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//
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// Test with paired-end data
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//
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workflow test_trimmomatic_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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TRIMMOMATIC_PE ( input )
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}
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//
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// Failing test with no adaptor
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//
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workflow test_trimmomatic_no_adaptor {
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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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TRIMMOMATIC ( input )
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}
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