diff --git a/modules/bcftools/roh/main.nf b/modules/bcftools/roh/main.nf index 890b6fad..83ac4e65 100644 --- a/modules/bcftools/roh/main.nf +++ b/modules/bcftools/roh/main.nf @@ -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 diff --git a/modules/bcftools/roh/meta.yml b/modules/bcftools/roh/meta.yml index fd03d4ce..fa0fd088 100644 --- a/modules/bcftools/roh/meta.yml +++ b/modules/bcftools/roh/meta.yml @@ -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." diff --git a/tests/modules/bcftools/roh/main.nf b/tests/modules/bcftools/roh/main.nf index 3eb534b6..3a2ef640 100644 --- a/tests/modules/bcftools/roh/main.nf +++ b/tests/modules/bcftools/roh/main.nf @@ -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 = []