mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
41 lines
1.3 KiB
Text
41 lines
1.3 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { BCFTOOLS_REHEADER } from '../../../../modules/bcftools/reheader/main.nf' addParams( options: [suffix: '.updated'] )
|
||
|
|
|
||
|
|
workflow test_bcftools_reheader_update_sequences {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ],
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
header = []
|
||
|
|
BCFTOOLS_REHEADER ( input, fai, header )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_bcftools_reheader_new_header {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ],
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
fai = []
|
||
|
|
header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
|
||
|
|
|
||
|
|
BCFTOOLS_REHEADER ( input, fai, header )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_bcftools_reheader_new_header_update_sequences {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ],
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
|
||
|
|
|
||
|
|
BCFTOOLS_REHEADER ( input, fai, header )
|
||
|
|
}
|