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7e8ad56688
* 1882 FASTP now supports interleaved FASTQ files Changes: - single_end FASTP pipes the FASTQ file - Using args, it can be configured for interleaved in `--interleaved_in` - Out is automatically interleaved if input is paired end. - Removed md5sum checks for FASTQ files as compression seemed to cause differences - Instead, we check inside the FASTQ files for content. Relates to #1882 Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
86 lines
2.6 KiB
Text
86 lines
2.6 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'
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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 intereleaved data
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//
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workflow test_fastp_interleaved {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_interleaved_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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