From 73aaecbc3ae62a124e1148b68b1a69dcfd9db0ed Mon Sep 17 00:00:00 2001
From: Michael L Heuer <heuermh@acm.org>
Date: Tue, 15 Mar 2022 11:02:40 -0500
Subject: [PATCH] Add BAM indexes as input for optitype module. (#1388)

---
 modules/optitype/main.nf        | 2 +-
 modules/optitype/meta.yml       | 4 ++++
 tests/config/test_data.config   | 3 ++-
 tests/modules/optitype/main.nf  | 3 ++-
 tests/modules/optitype/test.yml | 2 +-
 5 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/modules/optitype/main.nf b/modules/optitype/main.nf
index 984d4669..b6a3e200 100644
--- a/modules/optitype/main.nf
+++ b/modules/optitype/main.nf
@@ -8,7 +8,7 @@ process OPTITYPE {
         'quay.io/biocontainers/optitype:1.3.5--0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(bai)
 
     output:
     tuple val(meta), path("${prefix}"), emit: output
diff --git a/modules/optitype/meta.yml b/modules/optitype/meta.yml
index 4cacadda..9ca10774 100644
--- a/modules/optitype/meta.yml
+++ b/modules/optitype/meta.yml
@@ -22,6 +22,10 @@ input:
       type: file
       description: BAM file
       pattern: "*.{bam}"
+  - bai:
+      type: file
+      description: BAM index file
+      pattern: "*.{bai}"
 
 output:
   - meta:
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index ed1e2861..0d61d1e9 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -192,7 +192,8 @@ params {
                 test_paired_end_umi_unsorted_bam                        = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam"
                 test_paired_end_umi_unsorted_tagged_bam                 = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam"
                 test_paired_end_hla                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
-
+                test_paired_end_hla_sorted_bam                          = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
+                test_paired_end_hla_sorted_bam_bai                      = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai"
                 test2_paired_end_sorted_bam                    = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
                 test2_paired_end_sorted_bam_bai                = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
                 test2_paired_end_name_sorted_bam               = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
diff --git a/tests/modules/optitype/main.nf b/tests/modules/optitype/main.nf
index 55b46f0a..6ed14d96 100644
--- a/tests/modules/optitype/main.nf
+++ b/tests/modules/optitype/main.nf
@@ -6,7 +6,8 @@ include { OPTITYPE } from '../../../modules/optitype/main.nf'
 
 workflow test_optitype {
     input = [ [ id:'test', seq_type:'dna' ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla'], checkIfExists: true)
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla_sorted_bam'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla_sorted_bam_bai'], checkIfExists: true)
             ]
 
     OPTITYPE ( input )
diff --git a/tests/modules/optitype/test.yml b/tests/modules/optitype/test.yml
index bb493077..0cbb99cb 100644
--- a/tests/modules/optitype/test.yml
+++ b/tests/modules/optitype/test.yml
@@ -6,4 +6,4 @@
     - path: output/optitype/test/test_coverage_plot.pdf
     - path: output/optitype/test/test_result.tsv
       contains:
-        - "1446"
+        - "1439"