Merge branch 'master' into add-raredisease-scout-upload

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 62.2.10
+current_version = 62.2.14
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "62.2.10"
+__version__ = "62.2.14"

cg/apps/tb/api.py

@@ -119,6 +119,7 @@ def add_pending_analysis(
         ticket: str = None,
         workflow_manager: str = WorkflowManager.Slurm,
         tower_workflow_id: str | None = None,
+        is_hidden: bool = False,
     ) -> TrailblazerAnalysis:
         request_body = {
             "case_id": case_id,
@@ -132,6 +133,7 @@ def add_pending_analysis(
             "ticket": ticket,
             "workflow_manager": workflow_manager,
             "tower_workflow_id": tower_workflow_id,
+            "is_hidden": is_hidden,
         }
         LOG.debug(f"Submitting job to Trailblazer: {request_body}")
         if response := self.query_trailblazer(

cg/meta/workflow/analysis.py

@@ -15,6 +15,7 @@
 from cg.constants.constants import (
     AnalysisType,
     CaseActions,
+    CustomerId,
     FileFormat,
     GenomeVersion,
     WorkflowManager,
@@ -292,6 +293,7 @@ def add_pending_trailblazer_analysis(
         ticket: str = self.status_db.get_latest_ticket_from_case(case_id)
         workflow: Workflow = self.workflow
         workflow_manager: str = self.get_workflow_manager()
+        is_case_for_development: bool = self._is_case_for_development(case_id)
         self.trailblazer_api.add_pending_analysis(
             analysis_type=application_type,
             case_id=case_id,
@@ -304,8 +306,13 @@ def add_pending_trailblazer_analysis(
             workflow=workflow,
             workflow_manager=workflow_manager,
             tower_workflow_id=tower_workflow_id,
+            is_hidden=is_case_for_development,
         )
 
+    def _is_case_for_development(self, case_id: str) -> bool:
+        case: Case = self.status_db.get_case_by_internal_id(case_id)
+        return case.customer.internal_id == CustomerId.CG_INTERNAL_CUSTOMER
+
     def _get_order_id_from_case_id(self, case_id) -> int:
         case: Case = self.status_db.get_case_by_internal_id(case_id)
         return case.latest_order.id

cg/services/illumina/post_processing/housekeeper_storage.py

@@ -15,7 +15,6 @@
     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
 
@@ -33,10 +32,6 @@ 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

@@ -68,10 +68,7 @@ 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
-                or sample.is_negative_control
-            ):
+            if sample_metric.base_passing_q30_percent >= q30_threshold:
                 total_reads_for_sample += sample_metric.total_reads_in_lane
 
         sample.reads = total_reads_for_sample

cg/store/models.py

@@ -3,7 +3,6 @@
 from enum import Enum
 from typing import Annotated
 
-from pydantic import ConfigDict
 from sqlalchemy import (
     BLOB,
     DECIMAL,
@@ -25,7 +24,6 @@
 from cg.constants.constants import (
     CaseActions,
     ControlOptions,
-    CustomerId,
     PrepCategory,
     SequencingQCStatus,
     SexOptions,
@@ -820,14 +818,6 @@ def has_reads(self) -> bool:
     def is_negative_control(self) -> bool:
         return self.control == ControlOptions.NEGATIVE
 
-    @property
-    def is_internal_negative_control(self) -> bool:
-        return self.is_negative_control and self.customer == CustomerId.CG_INTERNAL_CUSTOMER
-
-    @property
-    def is_external_negative_control(self) -> bool:
-        return self.is_negative_control and self.customer != CustomerId.CG_INTERNAL_CUSTOMER
-
     @property
     def flow_cells(self) -> list[Flowcell]:
         """Return the flow cells a sample has been sequenced on."""

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "62.2.10"
+version = "62.2.14"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"

tests/store/crud/update/test_update.py

@@ -1,7 +1,6 @@
 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 (
     IlluminaSampleSequencingMetrics,
@@ -87,30 +86,6 @@ 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],