mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
45 lines
2 KiB
Text
45 lines
2 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { BCFTOOLS_BGZIP } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
|
||
|
|
include { BCFTOOLS_TABIX } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
|
||
|
|
include { BCFTOOLS_ISEC } from '../../../../software/bcftools/isec/main.nf' addParams( options: ['args': '--nfiles +2 --output-type z --no-version'] )
|
||
|
|
include { BCFTOOLS_BGZIP as BCFTOOLS_BGZIP2 } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
|
||
|
|
include { BCFTOOLS_TABIX as BCFTOOLS_TABIX2 } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
|
||
|
|
include { BCFTOOLS_BGZIP as BCFTOOLS_BGZIP3 } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
|
||
|
|
include { BCFTOOLS_TABIX as BCFTOOLS_TABIX3 } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
|
||
|
|
|
||
|
|
workflow test_bcftools_isec {
|
||
|
|
|
||
|
|
def input1, input2, input3 = []
|
||
|
|
|
||
|
|
input1 = [ [ id:'test1' ], // meta map
|
||
|
|
file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
|
||
|
|
|
||
|
|
input2 = [ [ id:'test2' ], // meta map
|
||
|
|
file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
|
||
|
|
|
||
|
|
input3 = [ [ id:'test3' ], // meta map
|
||
|
|
file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
|
||
|
|
|
||
|
|
BCFTOOLS_BGZIP ( input1 )
|
||
|
|
BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
|
||
|
|
BCFTOOLS_BGZIP2 ( input2 )
|
||
|
|
BCFTOOLS_TABIX2 ( BCFTOOLS_BGZIP2.out.vcf )
|
||
|
|
BCFTOOLS_BGZIP3 ( input3 )
|
||
|
|
BCFTOOLS_TABIX3 ( BCFTOOLS_BGZIP3.out.vcf )
|
||
|
|
|
||
|
|
vcfs = BCFTOOLS_BGZIP.out.vcf
|
||
|
|
.mix( BCFTOOLS_BGZIP2.out.vcf )
|
||
|
|
.mix( BCFTOOLS_BGZIP3.out.vcf )
|
||
|
|
.map { [ it[1] ]}.collect().map { [ [id: 'test'], it ] }
|
||
|
|
|
||
|
|
tbis = BCFTOOLS_TABIX.out.tbi
|
||
|
|
.mix( BCFTOOLS_TABIX2.out.tbi )
|
||
|
|
.mix( BCFTOOLS_TABIX3.out.tbi )
|
||
|
|
.map { [ it[1] ]}.collect().map { [ [id: 'test'], it ] }
|
||
|
|
|
||
|
|
BCFTOOLS_ISEC ( vcfs.join(tbis) )
|
||
|
|
}
|