nf-core_modules/tests/modules/fastp/main.nf

74 lines
2.3 KiB
Text
Raw Normal View History

2021-02-01 13:02:06 +00:00
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { FASTP } from '../../../modules/fastp/main.nf' addParams( options: [:] )
2021-02-01 13:02:06 +00:00
//
// Test with single-end data
//
workflow test_fastp_single_end {
2021-02-01 13:02:06 +00:00
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 )
2021-02-01 13:02:06 +00:00
}
//
// Test with paired-end data
//
workflow test_fastp_paired_end {
2021-02-01 13:02:06 +00:00
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 )
2021-02-01 13:02:06 +00:00
}
//
// 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 )
}