Revert "Revert earlier changes (#3689)" (#3769)(patch)

### Changed
- Reverts the commit in PR #3689

cg/services/illumina/post_processing/housekeeper_storage.py

@@ -15,6 +15,7 @@
     get_undetermined_fastqs,
     rename_fastq_file_if_needed,
 )
+from cg.store.models import Sample
 from cg.store.store import Store
 from cg.utils.files import get_files_matching_pattern
 
@@ -32,6 +33,10 @@ def _should_fastq_path_be_stored_in_housekeeper(
     Check if a sample fastq file should be tracked in Housekeeper.
     Only fastq files that pass the q30 threshold should be tracked.
     """
+    sample: Sample = store.get_sample_by_internal_id(internal_id=sample_id)
+
+    if sample.is_negative_control:
+        return True
 
     lane = get_lane_from_sample_fastq(sample_fastq_path)
     q30_threshold: int = get_q30_threshold(sequencer_type)

cg/store/crud/update.py

@@ -68,7 +68,10 @@ def update_sample_reads_illumina(self, internal_id: str, sequencer_type: Sequenc
         q30_threshold: int = get_q30_threshold(sequencer_type)
 
         for sample_metric in sample_metrics:
-            if sample_metric.base_passing_q30_percent >= q30_threshold:
+            if (
+                sample_metric.base_passing_q30_percent >= q30_threshold
+                or sample.is_negative_control
+            ):
                 total_reads_for_sample += sample_metric.total_reads_in_lane
 
         sample.reads = total_reads_for_sample

tests/store/crud/update/test_update.py

@@ -1,6 +1,7 @@
 from datetime import datetime
 
 from cg.constants import SequencingRunDataAvailability
+from cg.constants.constants import ControlOptions
 from cg.constants.sequencing import Sequencers
 from cg.store.models import IlluminaSequencingRun, Sample, IlluminaSampleSequencingMetrics, Analysis
 from cg.store.store import Store
@@ -82,6 +83,30 @@ def test_update_sample_reads_illumina_fail_q30(
     assert sample.reads == 0
 
 
+def test_update_sample_reads_illumina_negative_control(
+    store_with_illumina_sequencing_data: Store, selected_novaseq_x_sample_ids: list[str]
+):
+    # GIVEN a store with Illumina Sequencing Runs and a sample id
+    sample: Sample = store_with_illumina_sequencing_data.get_sample_by_internal_id(
+        selected_novaseq_x_sample_ids[0]
+    )
+    assert sample.reads == 0
+    # GIVEN that the sample is a negative control sample
+    sample.control = ControlOptions.NEGATIVE
+
+    # WHEN updating the sample reads for a sequencing run
+    store_with_illumina_sequencing_data.update_sample_reads_illumina(
+        internal_id=selected_novaseq_x_sample_ids[0], sequencer_type=Sequencers.NOVASEQX
+    )
+
+    # THEN the total reads for the sample is updated
+    total_reads_for_sample: int = 0
+    sample_metrics: list[IlluminaSampleSequencingMetrics] = sample.sample_run_metrics
+    for sample_metric in sample_metrics:
+        total_reads_for_sample += sample_metric.total_reads_in_lane
+    assert sample.reads == total_reads_for_sample
+
+
 def test_update_sample_last_sequenced_at(
     store_with_illumina_sequencing_data: Store,
     selected_novaseq_x_sample_ids: list[str],