Validate 10x coverage

cg/meta/workflow/microsalt/quality_checker.py

@@ -6,9 +6,10 @@
 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_10x_coverage,
     is_valid_average_coverage,
     is_valid_duplication_rate,
-    is_valid_mapped_rate,
+    is_valid_mapping_rate,
     is_valid_median_insert_size,
     is_valid_total_reads,
     is_valid_total_reads_for_control,
@@ -39,10 +40,11 @@ def quality_control(self, run_dir_path: Path, lims_project: str):
 
     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)
-        valid_median_insert_size: bool = self.is_valid_median_insert_size(metrics)
-        valid_average_coverage: bool = self.is_valid_average_coverage(metrics)
+        valid_mapping: bool = self.is_valid_mapped_rate(metrics)
+        valid_duplication: bool = self.is_valid_duplication_rate(metrics)
+        valid_inserts: bool = self.is_valid_median_insert_size(metrics)
+        valid_coverage: bool = self.is_valid_average_coverage(metrics)
+        valid_10x_coverage: bool = self.is_valid_10x_coverage(metrics)
 
     def quality_control_case(self, sample_results: list[QualityResult]) -> bool:
         pass
@@ -158,14 +160,12 @@ def is_valid_total_reads(self, sample_id: str) -> bool:
         sample_reads: int = sample.reads
 
         if sample.control == ControlEnum.negative:
-            return is_valid_total_reads_for_control(
-                sample_reads=sample_reads, target_reads=target_reads
-            )
-        return is_valid_total_reads(sample_reads=sample_reads, target_reads=target_reads)
+            return is_valid_total_reads_for_control(reads=sample_reads, target_reads=target_reads)
+        return is_valid_total_reads(reads=sample_reads, target_reads=target_reads)
 
     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)
+        return is_valid_mapping_rate(mapped_rate)
 
     def is_valid_duplication_rate(self, metrics: SampleMetrics) -> bool:
         duplication_rate: float = metrics.picard_markduplicate.duplication_rate
@@ -178,3 +178,7 @@ def is_valid_median_insert_size(self, metrics: SampleMetrics) -> bool:
     def is_valid_average_coverage(self, metrics: SampleMetrics) -> bool:
         average_coverage: float = metrics.microsalt_samtools_stats.average_coverage
         return is_valid_average_coverage(average_coverage)
+
+    def is_valid_10x_coverage(self, metrics: SampleMetrics) -> bool:
+        coverage_10x: float = metrics.microsalt_samtools_stats.coverage_10x
+        return is_valid_10x_coverage(coverage_10x)

cg/meta/workflow/microsalt/utils.py

@@ -5,30 +5,34 @@
 from cg.meta.workflow.microsalt.models import QualityMetrics
 
 
-def is_valid_total_reads(sample_reads: int, target_reads: int) -> bool:
-    return sample_reads > target_reads * MicrosaltQC.TARGET_READS_FAIL_THRESHOLD
+def is_valid_total_reads(reads: int, target_reads: int) -> bool:
+    return reads > target_reads * MicrosaltQC.TARGET_READS_FAIL_THRESHOLD
 
 
-def is_valid_total_reads_for_control(sample_reads: int, target_reads: int) -> bool:
-    return sample_reads < target_reads * MicrosaltQC.NEGATIVE_CONTROL_READS_THRESHOLD
+def is_valid_total_reads_for_control(reads: int, target_reads: int) -> bool:
+    return reads < target_reads * MicrosaltQC.NEGATIVE_CONTROL_READS_THRESHOLD
 
 
-def is_valid_mapped_rate(sample_mapped_rate: float) -> bool:
-    return sample_mapped_rate > MicrosaltQC.MAPPED_RATE_THRESHOLD
+def is_valid_mapping_rate(mapping_rate: float) -> bool:
+    return mapping_rate > MicrosaltQC.MAPPED_RATE_THRESHOLD
 
 
-def is_valid_duplication_rate(sample_duplication_rate: float) -> bool:
-    return sample_duplication_rate < MicrosaltQC.DUPLICATION_RATE_THRESHOLD
+def is_valid_duplication_rate(duplication_rate: float) -> bool:
+    return 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 is_valid_median_insert_size(insert_size: int) -> bool:
+    return insert_size > MicrosaltQC.INSERT_SIZE_THRESHOLD
 
 
 def is_valid_average_coverage(average_coverage: float) -> bool:
     return average_coverage > MicrosaltQC.AVERAGE_COVERAGE_THRESHOLD
 
 
+def is_valid_10x_coverage(coverage_10x: float) -> bool:
+    return coverage_10x > MicrosaltQC.COVERAGE_10X_THRESHOLD
+
+
 def parse_quality_metrics(file_path: Path) -> QualityMetrics:
     data = read_json(file_path)
     return QualityMetrics.model_validate_json(data)

tests/meta/workflow/microsalt/test_quality_control.py

@@ -8,7 +8,7 @@ def test_sample_total_reads_passing():
 
     # WHEN checking if the sample has sufficient reads
     passes_reads_threshold = is_valid_total_reads(
-        sample_reads=sample_reads, target_reads=target_reads
+        reads=sample_reads, target_reads=target_reads
     )
 
     # THEN it passes
@@ -22,7 +22,7 @@ def test_sample_total_reads_failing():
 
     # WHEN checking if the sample has sufficient reads
     passes_reads_threshold = is_valid_total_reads(
-        sample_reads=sample_reads, target_reads=target_reads
+        reads=sample_reads, target_reads=target_reads
     )
 
     # THEN it fails
@@ -36,7 +36,7 @@ def test_sample_total_reads_failing_without_reads():
 
     # WHEN checking if the sample has sufficient reads
     passes_reads_threshold = is_valid_total_reads(
-        sample_reads=sample_reads, target_reads=target_reads
+        reads=sample_reads, target_reads=target_reads
     )
 
     # THEN it fails