Set Nallo production QC checks

cg/constants/nf_analysis.py

@@ -16,7 +16,8 @@ class NfTowerStatus(StrEnum):
 
 
 NALLO_METRIC_CONDITIONS: dict[str, dict[str, Any]] = {
-    "median_coverage": {"norm": "gt", "threshold": 25},
+    "median_coverage": {"norm": "gt", "threshold": 20},
+    "predicted_sex_sex_check": {"norm": "eq", "threshold": None},
 }
 
 RAREDISEASE_ADAPTER_BASES_PERCENTAGE_THRESHOLD = 0.005

cg/meta/workflow/nallo.py

@@ -2,6 +2,7 @@
 
 import logging
 from pathlib import Path
+from typing import Any
 
 from cg.constants import Workflow
 from cg.constants.constants import GenomeVersion, FileFormat
@@ -13,7 +14,7 @@
 from cg.models.cg_config import CGConfig
 from cg.models.nallo.nallo import NalloParameters, NalloSampleSheetEntry, NalloSampleSheetHeaders
 from cg.resources import NALLO_BUNDLE_FILENAMES_PATH
-from cg.store.models import CaseSample
+from cg.store.models import CaseSample, Sample
 
 LOG = logging.getLogger(__name__)
 
@@ -138,5 +139,12 @@ def get_bundle_filenames_path() -> Path:
         """Return Nallo bundle filenames path."""
         return NALLO_BUNDLE_FILENAMES_PATH
 
-    def get_workflow_metrics(self, metric_id: str) -> dict:
-        return NALLO_METRIC_CONDITIONS
+    def get_workflow_metrics(self, sample_id: str) -> dict:
+        sample: Sample = self.status_db.get_sample_by_internal_id(internal_id=sample_id)
+        metric_conditions: dict[str, dict[str, Any]] = dict(NALLO_METRIC_CONDITIONS)
+        self.set_order_sex_for_sample(sample, metric_conditions)
+        return metric_conditions
+
+    @staticmethod
+    def set_order_sex_for_sample(sample: Sample, metric_conditions: dict) -> None:
+        metric_conditions["predicted_sex_sex_check"]["threshold"] = sample.sex