Fix quality result model

Clinical-Genomics · Dec 12, 2023 · ec60b96 · ec60b96
1 parent 48e247b
commit ec60b96
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Showing 3 changed files with 8 additions and 4 deletions.
diff --git a/cg/meta/workflow/microsalt/models.py b/cg/meta/workflow/microsalt/models.py
@@ -44,5 +44,6 @@ class QualityMetrics(BaseModel):
 
 
 class QualityResult(BaseModel):
-    sample: Sample
+    sample_id: str
+    is_negative_control: bool
     passes_qc: bool
diff --git a/cg/meta/workflow/microsalt/quality_checker.py b/cg/meta/workflow/microsalt/quality_checker.py
@@ -40,7 +40,6 @@ def quality_control(self, run_dir_path: Path, lims_project: str):
         self.quality_control_case(sample_results)
 
     def quality_control_sample(self, sample_id: str, metrics: SampleMetrics) -> QualityResult:
-        sample = self.status_db.get_sample_by_internal_id(sample_id)
         valid_reads: bool = self.is_valid_total_reads(sample_id)
         valid_mapping: bool = self.is_valid_mapped_rate(metrics)
         valid_duplication: bool = self.is_valid_duplication_rate(metrics)
@@ -57,8 +56,12 @@ def quality_control_sample(self, sample_id: str, metrics: SampleMetrics) -> Qual
             and valid_10x_coverage
         )
 
+        sample = self.status_db.get_sample_by_internal_id(sample_id)
+        is_negative_control: bool = sample.control == ControlEnum.negative
+
         return QualityResult(
-            sample=sample,
+            sample_id=sample_id,
+            is_negative_control=is_negative_control,
             passed=sample_passes_qc,
         )
 

diff --git a/cg/meta/workflow/microsalt/utils.py b/cg/meta/workflow/microsalt/utils.py
@@ -41,5 +41,5 @@ def parse_quality_metrics(file_path: Path) -> QualityMetrics:
 
 def get_negative_control_result(results: list[QualityResult]) -> QualityResult:
     for result in results:
-        if result.sample.control == ControlEnum.negative:
+        if result.is_negative_control:
             return result