Validate median insert size

cg/constants/constants.py

@@ -214,6 +214,7 @@ class MicrosaltQC:
     QC_PERCENT_THRESHOLD_MWX: float = 0.1
     COVERAGE_10X_THRESHOLD: float = 0.75
     DUPLICATION_RATE_THRESHOLD: float = 0.8
+    INSERT_SIZE_THRESHOLD: int = 100
     MAPPED_RATE_THRESHOLD: float = 0.3
     NEGATIVE_CONTROL_READS_THRESHOLD: float = 0.2
     TARGET_READS: int = 6000000

cg/meta/workflow/microsalt/quality_checker.py

@@ -8,6 +8,7 @@
 from cg.meta.workflow.microsalt.utils import (
     is_valid_duplication_rate,
     is_valid_mapped_rate,
+    is_valid_median_insert_size,
     is_valid_total_reads,
     is_valid_total_reads_for_control,
     parse_quality_metrics,
@@ -166,3 +167,7 @@ def is_valid_mapped_rate(self, metrics: SampleMetrics) -> bool:
     def is_valid_duplication_rate(self, metrics: SampleMetrics) -> bool:
         duplication_rate: float = metrics.picard_markduplicate.duplication_rate
         return is_valid_duplication_rate(duplication_rate)
+
+    def is_valid_median_insert_size(self, metrics: SampleMetrics) -> bool:
+        insert_size: int = metrics.picard_markduplicate.insert_size
+        return is_valid_median_insert_size(insert_size)

cg/meta/workflow/microsalt/utils.py

@@ -21,6 +21,10 @@ def is_valid_duplication_rate(sample_duplication_rate: float) -> bool:
     return sample_duplication_rate < MicrosaltQC.DUPLICATION_RATE_THRESHOLD
 
 
+def is_valid_median_insert_size(sample_insert_size: int) -> bool:
+    return sample_insert_size > MicrosaltQC.INSERT_SIZE_THRESHOLD
+
+
 def parse_quality_metrics(file_path: Path) -> QualityMetrics:
     data = read_json(file_path)
     return QualityMetrics.model_validate_json(data)