mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 00:02:04 +00:00
a552d97849
* added sarscov2 vcf data; adjusted bcftools tests * updated README.md * deleted old VCF files; fixed mergevcfs * fixed tabix
27 lines
1 KiB
Text
27 lines
1 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_gatk4_mergevcfs {
|
|
def input = []
|
|
input = [ [ id:'test' ], // meta map
|
|
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true),
|
|
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf", checkIfExists: true) ] ]
|
|
|
|
ref_dict = file('tests/data/genomics/sarscov2/fasta/test_genome.dict', checkIfExists: true)
|
|
|
|
GATK4_MERGEVCFS ( input, ref_dict, false )
|
|
}
|
|
|
|
workflow test_gatk4_mergevcfs_refdict {
|
|
def input = []
|
|
input = [ [ id:'test' ], // meta map
|
|
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true),
|
|
file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf", checkIfExists: true) ] ]
|
|
|
|
ref_dict = file('tests/data/genomics/sarscov2/fasta/test_genome.dict', checkIfExists: true)
|
|
|
|
GATK4_MERGEVCFS ( input, ref_dict, true )
|
|
}
|