From 011a23f98ae8ae662835249428c3cc09c873d827 Mon Sep 17 00:00:00 2001
From: William Rowell <wrowell@pacificbiosciences.com>
Date: Fri, 13 Dec 2024 11:16:43 -0800
Subject: [PATCH] Added sex to sawfish_discover tests.

---
 wdl-ci.config.json   | 44 ++++++++++++++++++++++++++++++++++++++++++++
 workflows/wdl-common |  2 +-
 2 files changed, 45 insertions(+), 1 deletion(-)

diff --git a/wdl-ci.config.json b/wdl-ci.config.json
index aac5c05..87dbabc 100644
--- a/wdl-ci.config.json
+++ b/wdl-ci.config.json
@@ -2359,6 +2359,7 @@
           "tests": [
             {
               "inputs": {
+                "sex": "MALE",
                 "aligned_bam": "${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam",
                 "aligned_bam_index": "${resources_file_path}/inputs/HG002.GRCh38.chr6_10000000_20000000.bam.bai",
                 "ref_fasta": "${ref_fasta}",
@@ -2376,6 +2377,47 @@
                   ]
                 }
               }
+            },
+            {
+              "inputs": {
+                "sex": "MALE",
+                "aligned_bam": "${resources_file_path}/inputs/HG003.GRCh38.chr6_10000000_20000000.bam",
+                "aligned_bam_index": "${resources_file_path}/inputs/HG003.GRCh38.chr6_10000000_20000000.bam.bai",
+                "ref_fasta": "${ref_fasta}",
+                "ref_index": "${ref_index}",
+                "expected_male_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XY.bed",
+                "expected_female_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XX.bed",
+                "out_prefix": "HG003.GRCh38",
+                "runtime_attributes": "${default_runtime_attributes}"
+              },
+              "output_tests": {
+                "discover_tar": {
+                  "value": "${resources_file_path}/sawfish_discover/output/HG003/HG003.GRCh38.tar",
+                  "test_tasks": [
+                    "compare_file_basename"
+                  ]
+                }
+              }
+            },
+            {
+              "inputs": {
+                "aligned_bam": "${resources_file_path}/inputs/HG004.GRCh38.chr6_10000000_20000000.bam",
+                "aligned_bam_index": "${resources_file_path}/inputs/HG004.GRCh38.chr6_10000000_20000000.bam.bai",
+                "ref_fasta": "${ref_fasta}",
+                "ref_index": "${ref_index}",
+                "expected_male_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XY.bed",
+                "expected_female_bed": "${resources_file_path}/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XX.bed",
+                "out_prefix": "HG004.GRCh38",
+                "runtime_attributes": "${default_runtime_attributes}"
+              },
+              "output_tests": {
+                "discover_tar": {
+                  "value": "${resources_file_path}/sawfish_discover/output/HG004/HG004.GRCh38.tar",
+                  "test_tasks": [
+                    "compare_file_basename"
+                  ]
+                }
+              }
             }
           ]
         },
@@ -2396,6 +2438,7 @@
                 ],
                 "ref_fasta": "${ref_fasta}",
                 "ref_index": "${ref_index}",
+                "ref_name": "${ref_name}",
                 "out_prefix": "HG002.GRCh38.structural_variants",
                 "runtime_attributes": "${default_runtime_attributes}"
               },
@@ -2436,6 +2479,7 @@
                 ],
                 "ref_fasta": "${ref_fasta}",
                 "ref_index": "${ref_index}",
+                "ref_name": "${ref_name}",
                 "out_prefix": "HG002-trio.joint.GRCh38.structural_variants",
                 "runtime_attributes": "${default_runtime_attributes}"
               },
diff --git a/workflows/wdl-common b/workflows/wdl-common
index 26d0aa7..f2c349f 160000
--- a/workflows/wdl-common
+++ b/workflows/wdl-common
@@ -1 +1 @@
-Subproject commit 26d0aa7f8c19a6458b56eb8c4111f77dbb20d166
+Subproject commit f2c349f95391386d643bbdfde2b96f07c428b886