mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
6bb4a6a7ee
* Implement PLINK_EXTRACT module * fix plink version number * Update main.nf * Update test_data.config * Update modules/plink/extract/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * just use one channel * fix test with new channel input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
29 lines
961 B
Text
29 lines
961 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { PLINK_VCF } from '../../../../modules/plink/vcf/main.nf' addParams ( options: [args:'--make-bed --set-missing-var-ids @:#:\\$1:\\$2'])
|
|
include { PLINK_EXTRACT } from '../../../../modules/plink/extract/main.nf' addParams( options: [suffix:'.extract'] )
|
|
|
|
workflow test_plink_extract {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
|
|
]
|
|
|
|
PLINK_VCF ( input )
|
|
|
|
PLINK_VCF.out.bim
|
|
.splitText(file: 'variants.keep', keepHeader: false, by: 10)
|
|
.first()
|
|
.set { ch_variants }
|
|
|
|
PLINK_VCF.out.bed
|
|
.concat(PLINK_VCF.out.bim, PLINK_VCF.out.fam.concat(ch_variants))
|
|
.groupTuple()
|
|
.map{ meta, paths -> [meta, paths[0], paths[1], paths[2], paths[3]] }
|
|
.set { ch_extract }
|
|
|
|
PLINK_EXTRACT ( ch_extract )
|
|
}
|