mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 13:23:09 +00:00
47 lines
1.4 KiB
Text
47 lines
1.4 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { VCFTOOLS as VCFTOOLS_BASE} from '../../../software/vcftools/main.nf' addParams( options: ['args': '--freq'] )
|
||
|
|
include { VCFTOOLS as VCFTOOLS_OPTIONAL} from '../../../software/vcftools/main.nf' addParams( options: ['args': '--freq --exclude-bed'] )
|
||
|
|
|
||
|
|
workflow test_vcftools_vcf_base {
|
||
|
|
|
||
|
|
def input = []
|
||
|
|
input = [ [ id:'test' ], // meta map
|
||
|
|
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]
|
||
|
|
|
||
|
|
VCFTOOLS_BASE ( input, [], [] )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_vcftools_vcfgz_base {
|
||
|
|
|
||
|
|
def input = []
|
||
|
|
input = [ [ id:'test' ], // meta map
|
||
|
|
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true) ]
|
||
|
|
|
||
|
|
VCFTOOLS_BASE ( input, [], [] )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_vcftools_vcf_optional {
|
||
|
|
|
||
|
|
def input = []
|
||
|
|
def bed = file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true)
|
||
|
|
|
||
|
|
input = [ [ id:'test' ], // meta map
|
||
|
|
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]
|
||
|
|
|
||
|
|
VCFTOOLS_OPTIONAL ( input, bed, [] )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_vcftools_vcfgz_optional {
|
||
|
|
|
||
|
|
def input = []
|
||
|
|
def bed = file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true)
|
||
|
|
|
||
|
|
input = [ [ id:'test' ], // meta map
|
||
|
|
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true) ]
|
||
|
|
|
||
|
|
VCFTOOLS_OPTIONAL ( input, bed, [] )
|
||
|
|
}
|