millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2025-01-18 02:46:13 -05:00
Code Issues Releases Packages Activity

Merge pull request #1737 from genomic-medicine-sweden/update_roh

Browse source 
Update bcftools/roh
This commit is contained in:
Ramprasad Neethiraj 2022-06-08 15:10:45 +02:00 • committed by GitHub
commit 912bc1caf2
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
3 changed files with 6 additions and 3 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
modules/bcftools/roh/main.nf
View file

@ -9,7 +9,7 @@ process BCFTOOLS_ROH {
input:
tuple val(meta), path(vcf), path(tbi)
path af_file
tuple path(af_file), path(af_file_tbi)
path genetic_map
path regions_file
path samples_file

3
modules/bcftools/roh/meta.yml
View file

@ -23,6 +23,9 @@ input:
- af_file:
type: file
description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF."
- af_file_tbi:
type: file
description: "tbi index of af_file."
- genetic_map:
type: file
description: "Genetic map in the format required also by IMPUTE2."

4
tests/modules/bcftools/roh/main.nf
View file

@ -10,7 +10,7 @@ workflow test_bcftools_roh {
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
af_file = []
af_file = [[],[]]
gen_map = []
regions = []
targets = []
@ -25,7 +25,7 @@ workflow test_bcftools_roh_stub {
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
af_file = []
af_file = [[],[]]
gen_map = []
regions = []
targets = []