mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
31 lines
869 B
Text
31 lines
869 B
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf'
|
||
|
|
include { PLINK2_EXTRACT } from '../../../../modules/plink2/extract/main.nf'
|
||
|
|
|
||
|
|
workflow test_plink2_extract {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
PLINK2_VCF ( input )
|
||
|
|
|
||
|
|
PLINK2_VCF.out.pvar
|
||
|
|
.splitText(file: 'variants.keep', keepHeader: false, by: 10)
|
||
|
|
.last()
|
||
|
|
.set { ch_variants }
|
||
|
|
|
||
|
|
ch_variants.view()
|
||
|
|
|
||
|
|
PLINK2_VCF.out.pgen
|
||
|
|
.concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar.concat(ch_variants))
|
||
|
|
.groupTuple()
|
||
|
|
.map{ meta, paths -> [meta, paths[0], paths[1], paths[2], paths[3]] }
|
||
|
|
.set { ch_extract }
|
||
|
|
|
||
|
|
PLINK2_EXTRACT ( ch_extract )
|
||
|
|
}
|