mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
e687c7025a
* add plink2_extract * fix test yml path * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * compress output * add DOI * make outputs less ambiguous * update test for compressed output * brain is dumb * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
30 lines
869 B
Text
30 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 )
|
|
}
|