From f2990dbc81b8e9febcce72095beb39cb47a714da Mon Sep 17 00:00:00 2001
From: William Rowell <wrowell@pacificbiosciences.com>
Date: Tue, 17 Dec 2024 17:12:00 -0800
Subject: [PATCH] Added test for exclusion of NO_READS.

---
 wdl-ci.config.json | 43 ++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 42 insertions(+), 1 deletion(-)

diff --git a/wdl-ci.config.json b/wdl-ci.config.json
index 315c71b..435d53e 100644
--- a/wdl-ci.config.json
+++ b/wdl-ci.config.json
@@ -2415,7 +2415,7 @@
         },
         "run_pharmcat": {
           "key": "run_pharmcat",
-          "digest": "uknkltw6uwppbf5ttzrsifayz4pqplvi",
+          "digest": "",
           "tests": [
             {
               "inputs": {
@@ -2457,6 +2457,47 @@
                   ]
                 }
               }
+            },
+            {
+              "inputs": {
+                "preprocessed_filtered_vcf": "${resources_file_path}/run_pharmcat/input/HG002.GRCh38.subset.small_variants.preprocessed.filtered.vcf",
+                "input_tsvs": [
+                  "${resources_file_path}/run_pharmcat/input/HG002.NO_READS.pharmcat.tsv"
+                ],
+                "pharmcat_docker": "pgkb/pharmcat:2.15.4",
+                "out_prefix": "HG002.pharmcat",
+                "runtime_attributes": "${default_runtime_attributes}"
+              },
+              "output_tests": {
+                "pharmcat_match_json": {
+                  "value": "${resources_file_path}/run_pharmcat/output/NO_READS/HG002.pharmcat.match.json",
+                  "test_tasks": [
+                    "compare_file_basename",
+                    "check_json"
+                  ]
+                },
+                "pharmcat_phenotype_json": {
+                  "value": "${resources_file_path}/run_pharmcat/output/NO_READS/HG002.pharmcat.phenotype.json",
+                  "test_tasks": [
+                    "compare_file_basename",
+                    "check_json"
+                  ]
+                },
+                "pharmcat_report_html": {
+                  "value": "${resources_file_path}/run_pharmcat/output/NO_READS/HG002.pharmcat.report.html",
+                  "test_tasks": [
+                    "compare_file_basename",
+                    "check_html"
+                  ]
+                },
+                "pharmcat_report_json": {
+                  "value": "${resources_file_path}/run_pharmcat/output/NO_READS/HG002.pharmcat.report.json",
+                  "test_tasks": [
+                    "compare_file_basename",
+                    "check_json"
+                  ]
+                }
+              }
             }
           ]
         }