mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
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
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { FASTP } from '../../../modules/fastp/main.nf' addParams( options: [:] )
|
|
|
|
//
|
|
// Test with single-end data
|
|
//
|
|
workflow test_fastp_single_end {
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
save_trimmed_fail = false
|
|
save_merged = false
|
|
|
|
FASTP ( input, save_trimmed_fail, save_merged )
|
|
}
|
|
|
|
//
|
|
// Test with paired-end data
|
|
//
|
|
workflow test_fastp_paired_end {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
save_trimmed_fail = false
|
|
save_merged = false
|
|
|
|
FASTP ( input, save_trimmed_fail, save_merged )
|
|
}
|
|
|
|
//
|
|
// Test with single-end data with saving trimming fails
|
|
//
|
|
workflow test_fastp_single_end_trim_fail {
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
save_trimmed_fail = true
|
|
save_merged = false
|
|
|
|
FASTP ( input, save_trimmed_fail, save_merged )
|
|
}
|
|
|
|
//
|
|
// Test with paired-end data with saving trimming fails
|
|
//
|
|
workflow test_fastp_paired_end_trim_fail {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
save_trimmed_fail = true
|
|
save_merged = false
|
|
|
|
FASTP ( input, save_trimmed_fail, save_merged )
|
|
}
|
|
|
|
//
|
|
// Test with paired-end data with merging
|
|
//
|
|
workflow test_fastp_paired_end_merged {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
save_trimmed_fail = false
|
|
save_merged = true
|
|
|
|
FASTP ( input, save_trimmed_fail, save_merged )
|
|
}
|