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

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Update bcftools/roh
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Ramprasad Neethiraj 2022-06-08 15:10:45 +02:00 committed by GitHub
commit 912bc1caf2
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3 changed files with 6 additions and 3 deletions
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2
modules/bcftools/roh/main.nf
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@ -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
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@ -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
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@ -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 = []