default conditions

Clinical-Genomics · Feb 1, 2022 · 5c2e1b6 · 5c2e1b6
1 parent 72f2331
commit 5c2e1b6
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Showing 4 changed files with 8 additions and 6 deletions.
diff --git a/BALSAMIC/constants/quality_check_reporting.py b/BALSAMIC/constants/quality_check_reporting.py
@@ -55,14 +55,14 @@
         "default": {
             "MEAN_INSERT_SIZE": {"condition": None},
             "PERCENT_DUPLICATION": {"condition": None},
-            "MEDIAN_TARGET_COVERAGE": {"condition": None},
+            "MEDIAN_TARGET_COVERAGE": {"condition": {"norm": "gt", "threshold": 500}},
             "PCT_TARGET_BASES_50X": {"condition": None},
             "PCT_TARGET_BASES_100X": {"condition": None},
             "PCT_TARGET_BASES_250X": {"condition": None},
             "PCT_TARGET_BASES_500X": {"condition": None},
             "PCT_TARGET_BASES_1000X": {"condition": None},
             "MEAN_TARGET_COVERAGE": {"condition": None},
-            "FOLD_80_BASE_PENALTY": {"condition": None},
+            "FOLD_80_BASE_PENALTY": {"condition": {"norm": "lt", "threshold": 1.8}},
             "PCT_OFF_BAIT": {"condition": None},
         },
         "gicfdna": {

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -7,6 +7,7 @@ Added:
 * Snakemake workflow to create canfam3 reference #843
 * Call umi variants using TNscope in bed defined regions #821
 * UMI duplication metrics to report in multiqc_picard_dups.json #844
+* QC default validation conditions (for not defined capture kits) #855
 
 Changed:
 ^^^^^^^^

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -523,6 +523,7 @@ def qc_requested_metrics():
             },
             "panel_2": {
                 "METRIC_1": {"condition": {"norm": "gt", "threshold": 1}},
+                "METRIC_2": {"condition": {"norm": "gt", "threshold": 22}},
                 "METRIC_4": {"condition": {"norm": "gt", "threshold": 4}},
             },
         },

diff --git a/tests/scripts/test_collect_qc_metrics.py b/tests/scripts/test_collect_qc_metrics.py
@@ -45,13 +45,13 @@ def test_get_requested_metrics_targeted(qc_requested_metrics):
 
     # GIVEN a sequencing type and a capture kit
     seq_type = "targeted"
-    capture_kit = "panel_1_v1.0_hg19_design.bed"
+    capture_kit = "panel_2_v1.0_hg19_design.bed"
 
     # GIVEN the expected output
     expected_output = {
-        "METRIC_1": {"condition": None},
-        "METRIC_2": {"condition": {"norm": "gt", "threshold": 2}},
-        "METRIC_3": {"condition": {"norm": "gt", "threshold": 3}},
+        "METRIC_1": {"condition": {"norm": "gt", "threshold": 1}},
+        "METRIC_2": {"condition": {"norm": "gt", "threshold": 22}},
+        "METRIC_4": {"condition": {"norm": "gt", "threshold": 4}},
     }
 
     # WHEN calling the function