mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
37 lines
1,002 B
Text
37 lines
1,002 B
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { NEXTGENMAP } from '../../../modules/nextgenmap/main.nf'
|
||
|
|
|
||
|
|
//
|
||
|
|
// Test with single-end data
|
||
|
|
//
|
||
|
|
workflow test_nextgenmap_single {
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:true ], // meta map
|
||
|
|
[
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
]
|
||
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
|
||
|
|
NEXTGENMAP ( input, fasta )
|
||
|
|
}
|
||
|
|
|
||
|
|
//
|
||
|
|
// Test with paired-end data
|
||
|
|
//
|
||
|
|
workflow test_bwamem2_mem_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)
|
||
|
|
]
|
||
|
|
]
|
||
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
|
||
|
|
NEXTGENMAP ( input, fasta )
|
||
|
|
}
|