Add validation of duplication rate

cg/constants/constants.py

@@ -213,6 +213,7 @@ class APIMethods(StrEnum):
 class MicrosaltQC:
     QC_PERCENT_THRESHOLD_MWX: float = 0.1
     COVERAGE_10X_THRESHOLD: float = 0.75
+    DUPLICATION_RATE_THRESHOLD: float = 0.8
     MAPPED_RATE_THRESHOLD: float = 0.3
     NEGATIVE_CONTROL_READS_THRESHOLD: float = 0.2
     TARGET_READS: int = 6000000

cg/meta/workflow/microsalt/quality_checker.py

@@ -6,6 +6,7 @@
 from cg.constants.constants import MicrosaltAppTags, MicrosaltQC
 from cg.meta.workflow.microsalt.models import QualityMetrics, QualityResult, SampleMetrics
 from cg.meta.workflow.microsalt.utils import (
+    is_valid_duplication_rate,
     is_valid_mapped_rate,
     is_valid_total_reads,
     is_valid_total_reads_for_control,
@@ -28,17 +29,16 @@ def quality_control(self, run_dir_path: Path, lims_project: str):
 
         sample_results: list[QualityResult] = []
 
-        for sample_metrics in quality_metrics:
-            result = self.quality_control_sample(sample_metrics)
+        for sample_id, metrics in quality_metrics:
+            result = self.quality_control_sample(sample_id=sample_id, metrics=metrics)
             sample_results.append(result)
 
         self.quality_control_case(sample_results)
 
-    def quality_control_sample(
-        self, sample_id: str, sample_metrics: SampleMetrics
-    ) -> QualityResult:
-        reads_passes_qc: bool = self.is_valid_total_reads(sample_id)
-        mapped_rate_passes_qc: bool = self.is_valid_mapped_rate(sample_metrics)
+    def quality_control_sample(self, sample_id: str, metrics: SampleMetrics) -> QualityResult:
+        valid_reads: bool = self.is_valid_total_reads(sample_id)
+        valid_mapped_rate: bool = self.is_valid_mapped_rate(metrics)
+        valid_duplication_rate: bool = self.is_valid_duplication_rate(metrics)
 
     def quality_control_case(self, sample_results: list[QualityResult]) -> bool:
         pass
@@ -162,3 +162,7 @@ def is_valid_total_reads(self, sample_id: str) -> bool:
     def is_valid_mapped_rate(self, metrics: SampleMetrics) -> bool:
         mapped_rate: float = metrics.microsalt_samtools_stats.mapped_rate
         return is_valid_mapped_rate(mapped_rate)
+
+    def is_valid_duplication_rate(self, metrics: SampleMetrics) -> bool:
+        duplication_rate: float = metrics.picard_markduplicate.duplication_rate
+        return is_valid_duplication_rate(duplication_rate)

cg/meta/workflow/microsalt/utils.py

@@ -17,6 +17,10 @@ def is_valid_mapped_rate(sample_mapped_rate: float) -> bool:
     return sample_mapped_rate > MicrosaltQC.MAPPED_RATE_THRESHOLD
 
 
+def is_valid_duplication_rate(sample_duplication_rate: float) -> bool:
+    return sample_duplication_rate < MicrosaltQC.DUPLICATION_RATE_THRESHOLD
+
+
 def parse_quality_metrics(file_path: Path) -> QualityMetrics:
     data = read_json(file_path)
     return QualityMetrics.model_validate_json(data)