mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 16:12:04 +00:00
32 lines
1.1 KiB
Text
32 lines
1.1 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { BCFTOOLS_QUERY } from '../../../../modules/bcftools/query/main.nf' addParams( options: ['args': "-f '%CHROM %POS %REF %ALT[%SAMPLE=%GT]'" ] )
|
||
|
|
|
||
|
|
workflow test_bcftools_query {
|
||
|
|
|
||
|
|
regions = []
|
||
|
|
targets = []
|
||
|
|
samples = []
|
||
|
|
|
||
|
|
input = [ [ id:'out' ], // meta map
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
|
||
|
|
|
||
|
|
BCFTOOLS_QUERY ( input, regions, targets, samples )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_bcftools_query_with_optional_files {
|
||
|
|
|
||
|
|
regions = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true)
|
||
|
|
targets = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true)
|
||
|
|
samples = []
|
||
|
|
|
||
|
|
input = [ [ id:'out' ], // meta map
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
|
||
|
|
|
||
|
|
BCFTOOLS_QUERY ( input, regions, targets, samples )
|
||
|
|
}
|