mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
a066456735
* NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
29 lines
819 B
Text
29 lines
819 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { UMITOOLS_EXTRACT } from '../../../../modules/umitools/extract/main.nf'
|
|
|
|
//
|
|
// Test with single-end data
|
|
//
|
|
workflow test_umitools_extract_single_end {
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
|
|
UMITOOLS_EXTRACT ( input )
|
|
}
|
|
|
|
//
|
|
// Test with paired-end data
|
|
//
|
|
workflow test_umitools_extract_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) ]
|
|
]
|
|
|
|
UMITOOLS_EXTRACT ( input )
|
|
}
|
|
|