chore: add QC criteria for lymphoma_MRD

BALSAMIC/assets/scripts/collect_qc_metrics.py

@@ -144,7 +144,14 @@ def get_qc_supported_capture_kit(capture_kit, metrics: List[str]) -> str:
         if k != "default":
             available_panel_beds.append(k)
 
-    return next((i for i in available_panel_beds if i in capture_kit), None)
+    return next(
+        (
+            i
+            for i in available_panel_beds
+            if re.search(rf"{re.escape(i)}(?=_\d)", capture_kit)
+        ),
+        None,
+    )
 
 
 def get_requested_metrics(config: dict, metrics: dict) -> dict:

BALSAMIC/constants/metrics.py

@@ -54,6 +54,9 @@
         "lymphomatic": {
             "PCT_TARGET_BASES_500X": {"condition": {"norm": "gt", "threshold": 0.90}},
         },
+        "lymphoma_MRD": {
+            "PCT_TARGET_BASES_1000X": {"condition": {"norm": "gt", "threshold": 0.95}},
+        },
         "probio": {
             "PCT_TARGET_BASES_250X": {"condition": {"norm": "gt", "threshold": 0.95}},
         },

CHANGELOG.rst

@@ -5,6 +5,8 @@ Added:
 ^^^^^^
 * MSIsensor-pro container https://github.com/Clinical-Genomics/BALSAMIC/pull/1444
 * MSI analysis to the tumor-normal workflow https://github.com/Clinical-Genomics/BALSAMIC/pull/1454
+* Sentieon install directory path to case config arguments https://github.com/Clinical-Genomics/BALSAMIC/pull/1461
+* QC threshold for lymphoma_MRD panel https://github.com/Clinical-Genomics/BALSAMIC/pull/1479
 * Sentieon install directory path to case config arguments https://giithub.com/Clinical-Genomics/BALSAMIC/pull/1461
 * MSI tumor-normal analysis to housekeeper storage https://github.com/Clinical-Genomics/BALSAMIC/pull/1483
 

tests/conftest.py

@@ -1909,10 +1909,10 @@ def qc_requested_metrics():
                 "METRIC_1": {"condition": None},
                 "METRIC_2": {"condition": {"norm": "gt", "threshold": 2}},
             },
-            "panel_1": {
+            "panelA": {
                 "METRIC_3": {"condition": {"norm": "gt", "threshold": 3}},
             },
-            "panel_2": {
+            "panelB": {
                 "METRIC_1": {"condition": {"norm": "gt", "threshold": 1}},
                 "METRIC_2": {"condition": {"norm": "gt", "threshold": 22}},
                 "METRIC_4": {"condition": {"norm": "gt", "threshold": 4}},

tests/scripts/test_collect_qc_metrics.py

@@ -23,10 +23,10 @@ def test_get_qc_supported_capture_kit(qc_requested_metrics):
     """test extraction of the capture kit name available for analysis"""
 
     # GIVEN a capture kit
-    capture_kit = "panel_1_v1.0_hg19_design.bed"
+    capture_kit = "panelA_1.0_hg19_design.bed"
 
     # GIVEN an expected output
-    expected_output = "panel_1"
+    expected_output = "panelA"
 
     # WHEN calling the function
     supported_capture_kit = get_qc_supported_capture_kit(
@@ -42,7 +42,7 @@ def test_get_requested_metrics_targeted(config_dict, qc_requested_metrics):
 
     # GIVEN a config_dict
     config = copy.deepcopy(config_dict)
-    config["panel"]["capture_kit"] = "tests/panel/panel_2_v1.0_hg19_design.bed"
+    config["panel"]["capture_kit"] = "tests/panel/panelB_1.0_hg19_design.bed"
 
     # GIVEN the expected output
     expected_output = {