mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
17dbff52f4
* added gatk4 variantfiltration * replace merge with filter * Update software/gatk4/variantfiltration/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * updated input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
18 lines
813 B
Text
18 lines
813 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
test_options = ['args': '--filter-name "test_filter" --filter-expression "MQ0 > 0"']
|
|
include { GATK4_VARIANTFILTRATION } from '../../../../software/gatk4/variantfiltration/main.nf' addParams( options: test_options )
|
|
|
|
workflow test_gatk4_variantfiltration {
|
|
def input = []
|
|
input = [ [ id:'test' ], // meta map
|
|
[ file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true)] ]
|
|
|
|
fasta = [ file("tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true),
|
|
file("tests/data/genomics/sarscov2/fasta/test_genome.fasta.fai", checkIfExists: true),
|
|
file("tests/data/genomics/sarscov2/fasta/test_genome.dict", checkIfExists: true)]
|
|
|
|
GATK4_VARIANTFILTRATION ( input, fasta )
|
|
}
|