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6f561b3b41
* enhance module fastp: add `save_merged` (#598) * removed md5sum checks from log and json
73 lines
2.3 KiB
Text
73 lines
2.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FASTP } from '../../../modules/fastp/main.nf' addParams( options: [:] )
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//
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// Test with single-end data
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//
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workflow test_fastp_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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save_trimmed_fail = false
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save_merged = false
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FASTP ( input, save_trimmed_fail, save_merged )
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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_fastp_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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save_trimmed_fail = false
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save_merged = false
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FASTP ( input, save_trimmed_fail, save_merged )
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}
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//
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// Test with single-end data with saving trimming fails
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//
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workflow test_fastp_single_end_trim_fail {
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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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save_trimmed_fail = true
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save_merged = false
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FASTP ( input, save_trimmed_fail, save_merged )
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}
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//
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// Test with paired-end data with saving trimming fails
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//
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workflow test_fastp_paired_end_trim_fail {
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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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save_trimmed_fail = true
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save_merged = false
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FASTP ( input, save_trimmed_fail, save_merged )
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}
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//
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// Test with paired-end data with merging
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//
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workflow test_fastp_paired_end_merged {
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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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save_trimmed_fail = false
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save_merged = true
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FASTP ( input, save_trimmed_fail, save_merged )
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}
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