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Clinical-Genomics · Dec 12, 2023 · 0227515 · 0227515
1 parent 71634c0
commit 0227515
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Showing 3 changed files with 18 additions and 11 deletions.
diff --git a/cg/meta/workflow/microsalt/models.py b/cg/meta/workflow/microsalt/models.py
@@ -44,4 +44,3 @@ class QualityMetrics(BaseModel):
 class QualityResult(BaseModel):
     sample_id: str
     passed: bool
-    fail_message: str | None = None
diff --git a/cg/meta/workflow/microsalt/quality_checker.py b/cg/meta/workflow/microsalt/quality_checker.py
@@ -46,8 +46,22 @@ def quality_control_sample(self, sample_id: str, metrics: SampleMetrics) -> Qual
         valid_coverage: bool = self.is_valid_average_coverage(metrics)
         valid_10x_coverage: bool = self.is_valid_10x_coverage(metrics)
 
+        sample_passes_qc: bool = (
+            valid_reads
+            and valid_mapping
+            and valid_duplication
+            and valid_inserts
+            and valid_coverage
+            and valid_10x_coverage
+        )
+
+        return QualityResult(
+            sample_id=sample_id,
+            passed=sample_passes_qc,
+        )
+
     def quality_control_case(self, sample_results: list[QualityResult]) -> bool:
-        pass
+        negative_control_passes: bool = True
 
     def microsalt_qc(self, case_id: str, run_dir_path: Path, lims_project: str) -> bool:
         """Check if given microSALT case passes QC check."""

diff --git a/tests/meta/workflow/microsalt/test_quality_control.py b/tests/meta/workflow/microsalt/test_quality_control.py
@@ -7,9 +7,7 @@ def test_sample_total_reads_passing():
     target_reads = 100
 
     # WHEN checking if the sample has sufficient reads
-    passes_reads_threshold = is_valid_total_reads(
-        reads=sample_reads, target_reads=target_reads
-    )
+    passes_reads_threshold = is_valid_total_reads(reads=sample_reads, target_reads=target_reads)
 
     # THEN it passes
     assert passes_reads_threshold
@@ -21,9 +19,7 @@ def test_sample_total_reads_failing():
     target_reads = 100
 
     # WHEN checking if the sample has sufficient reads
-    passes_reads_threshold = is_valid_total_reads(
-        reads=sample_reads, target_reads=target_reads
-    )
+    passes_reads_threshold = is_valid_total_reads(reads=sample_reads, target_reads=target_reads)
 
     # THEN it fails
     assert not passes_reads_threshold
@@ -35,9 +31,7 @@ def test_sample_total_reads_failing_without_reads():
     target_reads = 100
 
     # WHEN checking if the sample has sufficient reads
-    passes_reads_threshold = is_valid_total_reads(
-        reads=sample_reads, target_reads=target_reads
-    )
+    passes_reads_threshold = is_valid_total_reads(reads=sample_reads, target_reads=target_reads)
 
     # THEN it fails
     assert not passes_reads_threshold