From ea4dc866e09834704302c7f4cd8dd0401678b2e7 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Wed, 8 Jun 2022 14:38:55 +0200
Subject: [PATCH 1/2] add index

---
 modules/bcftools/roh/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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

From c079ee20250f5676c53b145fdd00f9defe91f112 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Wed, 8 Jun 2022 14:48:16 +0200
Subject: [PATCH 2/2] fix test

---
 modules/bcftools/roh/meta.yml      | 3 +++
 tests/modules/bcftools/roh/main.nf | 4 ++--
 2 files changed, 5 insertions(+), 2 deletions(-)

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 = []