mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
34 lines
1.1 KiB
Text
34 lines
1.1 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
|
||
|
|
include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
|
||
|
|
|
||
|
|
//
|
||
|
|
// Test with single-end data
|
||
|
|
//
|
||
|
|
workflow test_bwa_aln_single_end {
|
||
|
|
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)
|
||
|
|
|
||
|
|
BWA_INDEX ( fasta )
|
||
|
|
BWA_ALN ( input, BWA_INDEX.out.index )
|
||
|
|
}
|
||
|
|
|
||
|
|
//
|
||
|
|
// Test with paired-end data
|
||
|
|
//
|
||
|
|
workflow test_bwa_aln_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)
|
||
|
|
|
||
|
|
BWA_INDEX ( fasta )
|
||
|
|
BWA_ALN ( input, BWA_INDEX.out.index )
|
||
|
|
}
|