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c1eb9cce44
* Trimmomatic main only first draft * Add test files * SE PE Adjustment * Remove extra reads input * chore: Remove TODOs * Apply suggestions from code review Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * fix(trimmomatic): Handle SE output correctly Since there's never going to be unpaired reads for SE reads we can get away with it for SE * fix(trimmomatic): Use correct elvis operator to handle logic * fix(trimmomatic): Add hack to work with SE and PE reads * Update test.yml * use the PE and SE trimming correctly * Made user set adaptors * Add documentation * test(trimmomatic): Add files to pytest_modules * test(trimmomatic): Update name of failing test Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
42 lines
1.2 KiB
Text
42 lines
1.2 KiB
Text
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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