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https://github.com/MillironX/nf-core_modules.git
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625098a408
* fix: remove left-over unnecessary code * Partial fix for AR module output declarations * Remove `def` for prefix so useable in output block * Fix tests * Add adapterlist support * Fix tests after addition of adapter list
34 lines
1.2 KiB
Text
34 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ADAPTERREMOVAL } from '../../../modules/adapterremoval/main.nf'
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_COLLAPSE } from '../../../modules/adapterremoval/main.nf'
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workflow test_adapterremoval_single_end {
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input = [ [ id:'test', single_end:true, collapse:false ], // 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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ADAPTERREMOVAL ( input, [] )
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}
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workflow test_adapterremoval_paired_end {
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input = [ [ id:'test', single_end:false, collapse: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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ADAPTERREMOVAL ( input, [] )
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}
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workflow test_adapterremoval_paired_end_collapse {
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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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ADAPTERREMOVAL_COLLAPSE ( input, [] )
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}
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