add ngsbits sex check (#3752)

### Added
- ngs-bits sex check to raredisease

Author: peterpru

cg/constants/nf_analysis.py

@@ -22,6 +22,7 @@ class NfTowerStatus(StrEnum):
     "PCT_TARGET_BASES_10X": {"norm": "gt", "threshold": 0.95},
     "PCT_EXC_ADAPTER": {"norm": "lt", "threshold": 0.0005},
     "predicted_sex_sex_check": {"norm": "eq", "threshold": None},
+    "gender": {"norm": "eq", "threshold": None},
 }
 
 RAREDISEASE_PARENT_PEDDY_METRIC_CONDITION: dict[str, dict[str, Any]] = {

cg/meta/workflow/raredisease.py

@@ -218,6 +218,7 @@ def get_multiqc_json_metrics(self, case_id: str) -> list[MetricsBase]:
     @staticmethod
     def set_order_sex_for_sample(sample: Sample, metric_conditions: dict) -> None:
         metric_conditions["predicted_sex_sex_check"]["threshold"] = sample.sex
+        metric_conditions["gender"]["threshold"] = sample.sex
 
     def get_sample_coverage_file_path(self, bundle_name: str, sample_id: str) -> str | None:
         """Return the Raredisease d4 coverage file path."""

tests/fixtures/analysis/raredisease/multiqc_data.json

@@ -100,6 +100,14 @@
                 "summed_median": 327
             }
         },
+        {
+            "ADM1": {
+                "gender": "female",
+                "reads_chry": 103876,
+                "reads_chrx": 37077016,
+                "ratio_chry_chrx": 0.0028
+            }
+        },
         {
             "ADM1": {
                 "GENOME_TERRITORY": 2858674663.0,
@@ -301,6 +309,14 @@
                 "summed_median": 327
             }
         },
+        {
+            "ADM2": {
+                "gender": "female",
+                "reads_chry": 103876,
+                "reads_chrx": 37077016,
+                "ratio_chry_chrx": 0.0028
+            }
+        },
         {
             "ADM2": {
                 "GENOME_TERRITORY": 2858674663.0,

tests/fixtures/analysis/raredisease/raredisease_case_enough_reads_metrics_deliverables.yaml

@@ -563,6 +563,36 @@ metrics:
   name: summed_median
   step: multiqc
   value: 327
+- condition:
+    norm: eq
+    threshold: female
+  header: null
+  id: ADM1
+  input: multiqc_data.json
+  name: gender
+  step: multiqc
+  value: female
+- condition: null
+  header: null
+  id: ADM1
+  input: multiqc_data.json
+  name: reads_chry
+  step: multiqc
+  value: 103876
+- condition: null
+  header: null
+  id: ADM1
+  input: multiqc_data.json
+  name: reads_chrx
+  step: multiqc
+  value: 37077016
+- condition: null
+  header: null
+  id: ADM1
+  input: multiqc_data.json
+  name: ratio_chry_chrx
+  step: multiqc
+  value: 0.0028
 - condition: null
   header: null
   id: ADM1
@@ -1653,6 +1683,36 @@ metrics:
   name: summed_median
   step: multiqc
   value: 327
+- condition:
+    norm: eq
+    threshold: female
+  header: null
+  id: ADM2
+  input: multiqc_data.json
+  name: gender
+  step: multiqc
+  value: female
+- condition: null
+  header: null
+  id: ADM2
+  input: multiqc_data.json
+  name: reads_chry
+  step: multiqc
+  value: 103876
+- condition: null
+  header: null
+  id: ADM2
+  input: multiqc_data.json
+  name: reads_chrx
+  step: multiqc
+  value: 37077016
+- condition: null
+  header: null
+  id: ADM2
+  input: multiqc_data.json
+  name: ratio_chry_chrx
+  step: multiqc
+  value: 0.0028
 - condition: null
   header: null
   id: ADM2