Add reads qc to non microbial samples in microsalt (#2834)(patch)

Clinical-Genomics · Jan 12, 2024 · 3b132bc · 3b132bc
1 parent ad892a7
commit 3b132bc
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/cg/meta/workflow/microsalt/quality_controller/quality_controller.py b/cg/meta/workflow/microsalt/quality_controller/quality_controller.py
@@ -54,6 +54,7 @@ def quality_control_samples(self, quality_metrics: QualityMetrics) -> list[Sampl
         return sample_results
 
     def quality_control_sample(self, sample_id: str, metrics: SampleMetrics) -> SampleQualityResult:
+        """Perform a quality control of a sample given its metrics."""
         valid_read_count: bool = self.has_valid_total_reads(sample_id)
         valid_mapping: bool = has_valid_mapping_rate(metrics)
         valid_duplication: bool = has_valid_duplication_rate(metrics)
@@ -85,7 +86,7 @@ def quality_control_sample(self, sample_id: str, metrics: SampleMetrics) -> Samp
         )
 
         if has_non_microbial_apptag(sample):
-            sample_passes_qc = True
+            sample_passes_qc = valid_read_count
 
         sample_quality = SampleQualityResult(
             sample_id=sample_id,