Change logic, first adapt all indexes, then all barcode mismatches

cg/apps/demultiplex/sample_sheet/sample_models.py

@@ -38,12 +38,15 @@ def separate_indexes(self) -> None:
             self.index2 = index2.strip()
 
     @abstractmethod
-    def process_sample_for_sample_sheet(
-        self, run_parameters: RunParameters, samples_to_compare: list | None = None
-    ):
+    def process_indexes(self, run_parameters: RunParameters):
         """Update the required attributes to be exported to a sample sheet."""
         pass
 
+    @abstractmethod
+    def update_barcode_mismatches(self, samples_to_compare: list) -> None:
+        """Update the barcode_mismatches_1 and barcode_mismatches_2 attributes."""
+        pass
+
 
 class FlowCellSampleBcl2Fastq(FlowCellSample):
     """Base class for NovaSeq6000 flow cell samples."""
@@ -81,14 +84,18 @@ def _pad_indexes_if_necessary(self, run_parameters: RunParameters) -> None:
             return
         LOG.debug(f"Padding not necessary for sample {self.sample_id}")
 
-    def process_sample_for_sample_sheet(self, run_parameters: RunParameters, **kwargs):
+    def process_indexes(self, run_parameters: RunParameters):
         """Update the required attributes to be exported to a sample sheet."""
         reverse_index2: bool = run_parameters.index_settings.should_i5_be_reverse_complimented
         self.separate_indexes()
         self._pad_indexes_if_necessary(run_parameters=run_parameters)
         if reverse_index2:
             self.index2 = get_reverse_complement_dna_seq(self.index2)
 
+    def update_barcode_mismatches(self, samples_to_compare: list) -> None:
+        """No updating of barcode mismatch  values for Bcl2Fastq sample."""
+        LOG.debug(f"No updating of barcode mismatch values for Bcl2Fastq sample {self.sample_id}")
+
 
 class FlowCellSampleBCLConvert(FlowCellSample):
     """Class that represents a NovaSeqX flow cell sample."""
@@ -145,7 +152,7 @@ def update_override_cycles(self, run_parameters: RunParameters) -> None:
         )
         self.override_cycles = read1_cycles + index1_cycles + index2_cycles + read2_cycles
 
-    def update_barcode_mismatches_1(self, samples_to_compare: list) -> None:
+    def _update_barcode_mismatches_1(self, samples_to_compare: list) -> None:
         """Assign zero to barcode_mismatches_1 if the hamming distance between self.index
         and the index1 of any sample in the lane is below the minimum threshold."""
         for sample in samples_to_compare:
@@ -159,7 +166,7 @@ def update_barcode_mismatches_1(self, samples_to_compare: list) -> None:
                 self.barcode_mismatches_1 = 0
                 break
 
-    def update_barcode_mismatches_2(self, samples_to_compare: list) -> None:
+    def _update_barcode_mismatches_2(self, samples_to_compare: list) -> None:
         """Assign zero to barcode_mismatches_2 if the hamming distance between self.index2
         and the index2 of any sample in the lane is below the minimum threshold.
         If the sample is single-indexed, assign 'na'."""
@@ -178,15 +185,16 @@ def update_barcode_mismatches_2(self, samples_to_compare: list) -> None:
                 self.barcode_mismatches_2 = 0
                 break
 
-    def process_sample_for_sample_sheet(
-        self, run_parameters: RunParameters, samples_to_compare: list | None = None
-    ):
+    def process_indexes(self, run_parameters: RunParameters):
         """Update the required attributes to be exported to a sample sheet."""
-        if not samples_to_compare:
-            raise SampleSheetError("No samples to compare with to update barcode mismatch values")
         self.separate_indexes()
         if run_parameters.index_settings.should_i5_be_reverse_complimented:
             self.index2 = get_reverse_complement_dna_seq(self.index2)
-        self.update_override_cycles(run_parameters)
-        self.update_barcode_mismatches_1(samples_to_compare=samples_to_compare)
-        self.update_barcode_mismatches_2(samples_to_compare=samples_to_compare)
+        self.update_override_cycles(run_parameters=run_parameters)
+
+    def update_barcode_mismatches(self, samples_to_compare: list) -> None:
+        """Update the barcode_mismatches_1 and barcode_mismatches_2 attributes."""
+        if not samples_to_compare:
+            raise SampleSheetError("No samples to compare with to update barcode mismatch values")
+        self._update_barcode_mismatches_1(samples_to_compare=samples_to_compare)
+        self._update_barcode_mismatches_2(samples_to_compare=samples_to_compare)

cg/apps/demultiplex/sample_sheet/sample_sheet_creator.py

@@ -138,16 +138,12 @@ def create_sample_sheet_content(self) -> list[list[str]]:
     def process_samples_for_sample_sheet(self) -> None:
         """Remove unwanted samples and adapt remaining samples."""
         self.remove_unwanted_samples()
-        samples_in_lane: list[FlowCellSampleBCLConvert | FlowCellSampleBcl2Fastq]
+        for sample in self.lims_samples:
+            sample.process_indexes(run_parameters=self.run_parameters)
         for lane, samples_in_lane in get_samples_by_lane(self.lims_samples).items():
-            LOG.info(
-                "Adapting index, override cycles and barcode mismatch values "
-                f"for samples in lane {lane}"
-            )
+            LOG.info(f"Updating barcode mismatch values for samples in lane {lane}")
             for sample in samples_in_lane:
-                sample.process_sample_for_sample_sheet(
-                    run_parameters=self.run_parameters, samples_to_compare=samples_in_lane
-                )
+                sample.update_barcode_mismatches(samples_to_compare=samples_in_lane)
 
     def construct_sample_sheet(self) -> list[list[str]]:
         """Construct and validate the sample sheet."""

tests/apps/demultiplex/conftest.py

@@ -56,18 +56,6 @@ def bcl2fastq_sample_sheet_creator(
     )
 
 
-@pytest.fixture
-def bcl_convert_sample_sheet_creator(
-    bcl_convert_flow_cell: FlowCellDirectoryData,
-    lims_novaseq_bcl_convert_samples: list[FlowCellSampleBCLConvert],
-) -> SampleSheetCreatorBCLConvert:
-    """Returns a sample sheet creator for version 2 sample sheets with dragen format."""
-    return SampleSheetCreatorBCLConvert(
-        flow_cell=bcl_convert_flow_cell,
-        lims_samples=lims_novaseq_bcl_convert_samples,
-    )
-
-
 # Sample sheet validation
 
 

tests/apps/demultiplex/test_sample_models.py

@@ -216,7 +216,7 @@ def test_update_barcode_mismatches_1(
     sample_to_update: FlowCellSampleBCLConvert = sample_list[0]
 
     # WHEN updating the barcode mismatches 1
-    sample_to_update.update_barcode_mismatches_1(samples_to_compare=sample_list)
+    sample_to_update._update_barcode_mismatches_1(samples_to_compare=sample_list)
 
     # THEN the barcode mismatches 1 are updated with the expected value
     assert sample_to_update.barcode_mismatches_1 == expected_barcode_mismatch
@@ -240,7 +240,7 @@ def test_update_barcode_mismatches_2(
     sample_to_update: FlowCellSampleBCLConvert = sample_list[0]
 
     # WHEN updating the barcode mismatches 2
-    sample_to_update.update_barcode_mismatches_2(samples_to_compare=sample_list)
+    sample_to_update._update_barcode_mismatches_2(samples_to_compare=sample_list)
 
     # THEN the barcode mismatches 1 are updated with the expected value
     assert sample_to_update.barcode_mismatches_2 == expected_barcode_mismatch
@@ -278,7 +278,7 @@ def test_process_sample_for_sample_sheet_bcl_convert(
     sample: FlowCellSampleBCLConvert = raw_lims_samples[0]
 
     # WHEN processing the sample for a sample sheet
-    sample.process_sample_for_sample_sheet(run_parameters=run_parameters)
+    sample.process_indexes(run_parameters=run_parameters)
 
     # THEN the sample is processed
     assert sample.barcode_mismatches_1

tests/cli/demultiplex/test_create_sample_sheet.py

@@ -122,7 +122,7 @@ class SampleSheetScenario(BaseModel):
         ),
         SampleSheetScenario(
             flow_cell_directory="novaseq_6000_post_1_5_kits_flow_cell",
-            lims_samples="novaseq_6000_post_1_5_kits_samples",
+            lims_samples="novaseq_6000_post_1_5_kits_lims_samples",
             correct_sample_sheet="novaseq_6000_post_1_5_kits_correct_sample_sheet",
         ),
         SampleSheetScenario(

tests/conftest.py

@@ -19,6 +19,7 @@
     FlowCellSampleBcl2Fastq,
     FlowCellSampleBCLConvert,
 )
+from cg.apps.demultiplex.sample_sheet.sample_sheet_creator import SampleSheetCreatorBCLConvert
 from cg.apps.downsample.downsample import DownsampleAPI
 from cg.apps.gens import GensAPI
 from cg.apps.gt import GenotypeAPI
@@ -1006,6 +1007,18 @@ def sample_sheet_context(
     return cg_context
 
 
+@pytest.fixture
+def bcl_convert_sample_sheet_creator(
+    bcl_convert_flow_cell: FlowCellDirectoryData,
+    lims_novaseq_bcl_convert_samples: list[FlowCellSampleBCLConvert],
+) -> SampleSheetCreatorBCLConvert:
+    """Returns a sample sheet creator for version 2 sample sheets with dragen format."""
+    return SampleSheetCreatorBCLConvert(
+        flow_cell=bcl_convert_flow_cell,
+        lims_samples=lims_novaseq_bcl_convert_samples,
+    )
+
+
 @pytest.fixture(scope="session")
 def bcl_convert_demultiplexed_flow_cell_sample_internal_ids() -> list[str]:
     """