diff --git a/tests/apps/demultiplex/conftest.py b/tests/apps/demultiplex/conftest.py index fcc3010561..45cba82e18 100644 --- a/tests/apps/demultiplex/conftest.py +++ b/tests/apps/demultiplex/conftest.py @@ -47,12 +47,12 @@ def bcl_convert_samples_similar_index2() -> list[FlowCellSampleBCLConvert]: @pytest.fixture def bcl2fastq_sample_sheet_creator( novaseq_flow_cell_demultiplexed_with_bcl2fastq: FlowCellDirectoryData, - lims_novaseq_6000_bcl2fastq_samples: list[FlowCellSampleBcl2Fastq], + novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples: list[FlowCellSampleBcl2Fastq], ) -> SampleSheetCreatorBcl2Fastq: """Returns a sample sheet creator for version 1 sample sheets with bcl2fastq format.""" return SampleSheetCreatorBcl2Fastq( flow_cell=novaseq_flow_cell_demultiplexed_with_bcl2fastq, - lims_samples=lims_novaseq_6000_bcl2fastq_samples, + lims_samples=novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples, ) diff --git a/tests/apps/demultiplex/test_sample_models.py b/tests/apps/demultiplex/test_sample_models.py index 6d9d30e4a3..8c43dc27b2 100644 --- a/tests/apps/demultiplex/test_sample_models.py +++ b/tests/apps/demultiplex/test_sample_models.py @@ -321,8 +321,14 @@ def test_update_barcode_mismatches_2( "run_parameters_fixture, raw_lims_samples_fixture", [ ("novaseq_x_run_parameters", "novaseq_x_lims_samples"), - ("novaseq_6000_run_parameters_pre_1_5_kits", "novaseq_6000_pre_1_5_kits_lims_samples"), - ("novaseq_6000_run_parameters_post_1_5_kits", "novaseq_6000_post_1_5_kits_lims_samples"), + ( + "novaseq_6000_run_parameters_pre_1_5_kits", + "novaseq_6000_pre_1_5_kits_bcl_convert_lims_samples", + ), + ( + "novaseq_6000_run_parameters_post_1_5_kits", + "novaseq_6000_post_1_5_kits_bcl_convert_lims_samples", + ), ("hiseq_x_single_index_run_parameters", "hiseq_x_single_index_bcl_convert_lims_samples"), ("hiseq_x_dual_index_run_parameters", "hiseq_x_dual_index_bcl_convert_lims_samples"), ("hiseq_2500_dual_index_run_parameters", "hiseq_2500_dual_index_bcl_convert_lims_samples"), diff --git a/tests/apps/demultiplex/test_sample_sheet_creator.py b/tests/apps/demultiplex/test_sample_sheet_creator.py index d733a94902..9226a48aa7 100644 --- a/tests/apps/demultiplex/test_sample_sheet_creator.py +++ b/tests/apps/demultiplex/test_sample_sheet_creator.py @@ -21,7 +21,7 @@ def test_bcl_convert_sample_sheet_fails_with_bcl2fastq( novaseq_x_flow_cell: FlowCellDirectoryData, - lims_novaseq_bcl_convert_samples: list[FlowCellSampleBCLConvert], + novaseq_x_lims_samples: list[FlowCellSampleBCLConvert], ): """Test that creating a BCL Convert sample sheet fails if the bcl converter is Bcl2fastq.""" # GIVEN a NovaSeqX flow cell and samples and the bcl converter is Bcl2fastq @@ -31,7 +31,7 @@ def test_bcl_convert_sample_sheet_fails_with_bcl2fastq( with pytest.raises(SampleSheetError) as exc_info: SampleSheetCreatorBCLConvert( flow_cell=novaseq_x_flow_cell, - lims_samples=lims_novaseq_bcl_convert_samples, + lims_samples=novaseq_x_lims_samples, ) # THEN an error is raised assert ( diff --git a/tests/apps/demultiplex/test_sample_sheet_creator_factory.py b/tests/apps/demultiplex/test_sample_sheet_creator_factory.py index 01f53d8d08..295fd11dcc 100644 --- a/tests/apps/demultiplex/test_sample_sheet_creator_factory.py +++ b/tests/apps/demultiplex/test_sample_sheet_creator_factory.py @@ -17,7 +17,7 @@ def test_sample_sheet_creator_factory_novaseq_6000( novaseq_flow_cell_demultiplexed_with_bcl2fastq: FlowCellDirectoryData, - lims_novaseq_bcl2fastq_samples: list[FlowCellSampleBcl2Fastq], + novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples: list[FlowCellSampleBcl2Fastq], ): """Test that a sample sheet creator defined with NovaSeq6000 data is V1.""" # GIVEN a NovaSeq6000 flow cell and a list of NovaSeq6000 samples @@ -28,7 +28,7 @@ def test_sample_sheet_creator_factory_novaseq_6000( # WHEN defining the sample sheet creator sample_sheet_creator: SampleSheetCreator = get_sample_sheet_creator( flow_cell=novaseq_flow_cell_demultiplexed_with_bcl2fastq, - lims_samples=lims_novaseq_bcl2fastq_samples, + lims_samples=novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples, force=False, ) @@ -36,18 +36,18 @@ def test_sample_sheet_creator_factory_novaseq_6000( assert isinstance(sample_sheet_creator, SampleSheetCreatorBcl2Fastq) -def test_sample_sheet_creator_factory_BCL_convert( +def test_sample_sheet_creator_factory_bcl_convert( novaseq_x_flow_cell: FlowCellDirectoryData, - lims_novaseq_bcl_convert_samples: list[FlowCellSampleBCLConvert], + novaseq_x_lims_samples: list[FlowCellSampleBCLConvert], ): """Test that a sample sheet creator defined with BCL convert data is BCL Convert.""" - # GIVEN a NovaSeqX flow cell and a list of NovaSeqX samples that is demultiplexed wit BCL Convert + # GIVEN a NovaSeqX flow cell and a list of NovaSeqX BCL Convert samples assert novaseq_x_flow_cell.bcl_converter == BclConverter.DRAGEN # WHEN defining the sample sheet creator sample_sheet_creator: SampleSheetCreator = get_sample_sheet_creator( flow_cell=novaseq_x_flow_cell, - lims_samples=lims_novaseq_bcl_convert_samples, + lims_samples=novaseq_x_lims_samples, force=False, ) diff --git a/tests/cli/demultiplex/test_create_sample_sheet.py b/tests/cli/demultiplex/test_create_sample_sheet.py index 72c1279da1..8ea1476e76 100644 --- a/tests/cli/demultiplex/test_create_sample_sheet.py +++ b/tests/cli/demultiplex/test_create_sample_sheet.py @@ -23,7 +23,7 @@ def test_create_sample_sheet_no_run_parameters_fails( cli_runner: testing.CliRunner, tmp_flow_cells_directory_no_run_parameters: Path, sample_sheet_context: CGConfig, - lims_novaseq_bcl2fastq_samples: list[FlowCellSampleBcl2Fastq], + novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples: list[FlowCellSampleBcl2Fastq], caplog, mocker, ): @@ -36,7 +36,7 @@ def test_create_sample_sheet_no_run_parameters_fails( # GIVEN flow cell samples mocker.patch( FLOW_CELL_FUNCTION_NAME, - return_value=lims_novaseq_bcl2fastq_samples, + return_value=novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples, ) # GIVEN that the context's flow cell directory holds the given flow cell @@ -60,7 +60,7 @@ def test_create_bcl2fastq_sample_sheet( cli_runner: testing.CliRunner, tmp_flow_cells_directory_no_sample_sheet: Path, sample_sheet_context: CGConfig, - lims_novaseq_bcl2fastq_samples: list[FlowCellSampleBcl2Fastq], + novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples: list[FlowCellSampleBcl2Fastq], mocker, ): """Test that creating a Bcl2fastq sample sheet works.""" @@ -82,7 +82,7 @@ def test_create_bcl2fastq_sample_sheet( # GIVEN flow cell samples mocker.patch( FLOW_CELL_FUNCTION_NAME, - return_value=lims_novaseq_bcl2fastq_samples, + return_value=novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples, ) # GIVEN a lims api that returns some samples @@ -116,14 +116,14 @@ class SampleSheetScenario(BaseModel): "scenario", [ SampleSheetScenario( - flow_cell_directory="novaseq_6000_pre_1_5_kits_flow_cell", - lims_samples="novaseq_6000_pre_1_5_kits_lims_samples", - correct_sample_sheet="novaseq_6000_pre_1_5_kits_correct_sample_sheet", + flow_cell_directory="novaseq_6000_pre_1_5_kits_flow_cell_path", + lims_samples="novaseq_6000_pre_1_5_kits_bcl_convert_lims_samples", + correct_sample_sheet="novaseq_6000_pre_1_5_kits_correct_sample_sheet_path", ), SampleSheetScenario( - flow_cell_directory="novaseq_6000_post_1_5_kits_flow_cell", - lims_samples="novaseq_6000_post_1_5_kits_lims_samples", - correct_sample_sheet="novaseq_6000_post_1_5_kits_correct_sample_sheet", + flow_cell_directory="novaseq_6000_post_1_5_kits_flow_cell_path", + lims_samples="novaseq_6000_post_1_5_kits_bcl_convert_lims_samples", + correct_sample_sheet="novaseq_6000_post_1_5_kits_correct_sample_sheet_path", ), SampleSheetScenario( flow_cell_directory="novaseq_x_flow_cell_directory", @@ -137,7 +137,6 @@ def test_create_dragen_sample_sheet( cli_runner: testing.CliRunner, scenario: SampleSheetScenario, sample_sheet_context: CGConfig, - lims_novaseq_bcl_convert_samples: list[FlowCellSampleBCLConvert], mocker, request: FixtureRequest, ): @@ -193,7 +192,7 @@ def test_incorrect_bcl2fastq_headers_samplesheet( cli_runner: testing.CliRunner, tmp_flow_cells_directory_malformed_sample_sheet: Path, sample_sheet_context: CGConfig, - lims_novaseq_bcl2fastq_samples: list[FlowCellSampleBcl2Fastq], + novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples: list[FlowCellSampleBcl2Fastq], mocker, caplog, ): @@ -207,7 +206,7 @@ def test_incorrect_bcl2fastq_headers_samplesheet( # GIVEN flow cell samples mocker.patch( FLOW_CELL_FUNCTION_NAME, - return_value=lims_novaseq_bcl2fastq_samples, + return_value=novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples, ) # GIVEN a lims api that returns some samples diff --git a/tests/fixture_plugins/demultiplex_fixtures/flow_cell_fixtures.py b/tests/fixture_plugins/demultiplex_fixtures/flow_cell_fixtures.py index 09213170bd..bca44c4711 100644 --- a/tests/fixture_plugins/demultiplex_fixtures/flow_cell_fixtures.py +++ b/tests/fixture_plugins/demultiplex_fixtures/flow_cell_fixtures.py @@ -92,10 +92,10 @@ def novaseq_6000_flow_cell(bcl_convert_flow_cell: FlowCellDirectoryData) -> Flow @pytest.fixture(scope="function") -def novaseq_x_flow_cell(novaseq_x_flow_cell_dir: Path) -> FlowCellDirectoryData: +def novaseq_x_flow_cell(novaseq_x_flow_cell_directory: Path) -> FlowCellDirectoryData: """Create a NovaSeqX flow cell object with flow cell that is demultiplexed.""" return FlowCellDirectoryData( - flow_cell_path=novaseq_x_flow_cell_dir, bcl_converter=BclConverter.DRAGEN + flow_cell_path=novaseq_x_flow_cell_directory, bcl_converter=BclConverter.DRAGEN ) diff --git a/tests/fixture_plugins/demultiplex_fixtures/path_fixtures.py b/tests/fixture_plugins/demultiplex_fixtures/path_fixtures.py index 807c34ee41..f5b305aa53 100644 --- a/tests/fixture_plugins/demultiplex_fixtures/path_fixtures.py +++ b/tests/fixture_plugins/demultiplex_fixtures/path_fixtures.py @@ -202,39 +202,27 @@ def demux_results_not_finished_dir(demultiplex_fixtures: Path) -> Path: @pytest.fixture -def novaseq_6000_post_1_5_kits_flow_cell(tmp_flow_cells_directory: Path) -> Path: +def novaseq_6000_post_1_5_kits_flow_cell_path(tmp_flow_cells_directory: Path) -> Path: return Path(tmp_flow_cells_directory, "230912_A00187_1009_AHK33MDRX3") @pytest.fixture -def novaseq_6000_post_1_5_kits_correct_sample_sheet( - novaseq_6000_post_1_5_kits_flow_cell: Path, +def novaseq_6000_post_1_5_kits_correct_sample_sheet_path( + novaseq_6000_post_1_5_kits_flow_cell_path: Path, ) -> Path: - return Path(novaseq_6000_post_1_5_kits_flow_cell, CORRECT_SAMPLE_SHEET) + return Path(novaseq_6000_post_1_5_kits_flow_cell_path, CORRECT_SAMPLE_SHEET) @pytest.fixture -def novaseq_6000_post_1_5_kits_raw_lims_samples( - novaseq_6000_post_1_5_kits_flow_cell: Path, -) -> Path: - return Path(novaseq_6000_post_1_5_kits_flow_cell, "HK33MDRX3_raw.json") - - -@pytest.fixture -def novaseq_6000_pre_1_5_kits_flow_cell(tmp_flow_cells_directory: Path) -> Path: +def novaseq_6000_pre_1_5_kits_flow_cell_path(tmp_flow_cells_directory: Path) -> Path: return Path(tmp_flow_cells_directory, "190927_A00689_0069_BHLYWYDSXX") @pytest.fixture -def novaseq_6000_pre_1_5_kits_correct_sample_sheet( - novaseq_6000_pre_1_5_kits_flow_cell: Path, +def novaseq_6000_pre_1_5_kits_correct_sample_sheet_path( + novaseq_6000_pre_1_5_kits_flow_cell_path: Path, ) -> Path: - return Path(novaseq_6000_pre_1_5_kits_flow_cell, CORRECT_SAMPLE_SHEET) - - -@pytest.fixture -def novaseq_6000_pre_1_5_kits_raw_lims_samples(novaseq_6000_pre_1_5_kits_flow_cell: Path) -> Path: - return Path(novaseq_6000_pre_1_5_kits_flow_cell, "HLYWYDSXX_raw.json") + return Path(novaseq_6000_pre_1_5_kits_flow_cell_path, CORRECT_SAMPLE_SHEET) @pytest.fixture @@ -247,11 +235,6 @@ def novaseq_x_correct_sample_sheet(novaseq_x_flow_cell_directory: Path) -> Path: return Path(novaseq_x_flow_cell_directory, CORRECT_SAMPLE_SHEET) -@pytest.fixture -def novaseq_x_raw_lims_samples(novaseq_x_flow_cell_directory: Path) -> Path: - return Path(novaseq_x_flow_cell_directory, "22F52TLT3_raw.json") - - @pytest.fixture(scope="session") def novaseq_x_manifest_file(novaseq_x_flow_cell_dir: Path) -> Path: """Return the path to a NovaSeqX manifest file.""" @@ -374,22 +357,22 @@ def novaseq_6000_run_parameters_path(bcl2fastq_flow_cell_dir: Path) -> Path: @pytest.fixture def novaseq_6000_run_parameters_pre_1_5_kits_path( - novaseq_6000_pre_1_5_kits_flow_cell: Path, + novaseq_6000_pre_1_5_kits_flow_cell_path: Path, ) -> Path: """Return the path to a NovaSeq6000 pre 1.5 kit run parameters file.""" return Path( - novaseq_6000_pre_1_5_kits_flow_cell, + novaseq_6000_pre_1_5_kits_flow_cell_path, DemultiplexingDirsAndFiles.RUN_PARAMETERS_PASCAL_CASE, ) @pytest.fixture def novaseq_6000_run_parameters_post_1_5_kits_path( - novaseq_6000_post_1_5_kits_flow_cell: Path, + novaseq_6000_post_1_5_kits_flow_cell_path: Path, ) -> Path: """Return the path to a NovaSeq6000 post 1.5 kit run parameters file.""" return Path( - novaseq_6000_post_1_5_kits_flow_cell, + novaseq_6000_post_1_5_kits_flow_cell_path, DemultiplexingDirsAndFiles.RUN_PARAMETERS_PASCAL_CASE, ) diff --git a/tests/fixture_plugins/demultiplex_fixtures/sample_fixtures.py b/tests/fixture_plugins/demultiplex_fixtures/sample_fixtures.py index 9973ddf58e..1a644238c7 100644 --- a/tests/fixture_plugins/demultiplex_fixtures/sample_fixtures.py +++ b/tests/fixture_plugins/demultiplex_fixtures/sample_fixtures.py @@ -1,4 +1,4 @@ -"""Demultiplex sample fixtures.""" +"""Fixtures for parsed raw LIMS samples for demultiplexing and sample sheet creation.""" from pathlib import Path import pytest @@ -9,83 +9,15 @@ ) from cg.apps.demultiplex.sample_sheet.sample_sheet_creator import SampleSheetCreatorBCLConvert from cg.constants import FileExtensions -from cg.constants.constants import FileFormat -from cg.io.controller import ReadFile from cg.io.json import read_json from cg.models.flow_cell.flow_cell import FlowCellDirectoryData -@pytest.fixture -def lims_novaseq_bcl_convert_samples( - lims_novaseq_samples_raw: list[dict], -) -> list[FlowCellSampleBCLConvert]: - """Return a list of parsed flow cell samples demultiplexed with BCL convert.""" - return [FlowCellSampleBCLConvert.model_validate(sample) for sample in lims_novaseq_samples_raw] - - -@pytest.fixture -def lims_novaseq_bcl2fastq_samples( - lims_novaseq_samples_raw: list[dict], -) -> list[FlowCellSampleBcl2Fastq]: - """Return a list of parsed Bcl2fastq flow cell samples""" - return [FlowCellSampleBcl2Fastq.model_validate(sample) for sample in lims_novaseq_samples_raw] - - -@pytest.fixture -def lims_novaseq_6000_bcl2fastq_samples( - lims_novaseq_6000_sample_raw: list[dict], -) -> list[FlowCellSampleBcl2Fastq]: - """Return a list of parsed Bcl2fastq flow cell samples""" - return [ - FlowCellSampleBcl2Fastq.model_validate(sample) for sample in lims_novaseq_6000_sample_raw - ] - - -@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 -def novaseq_6000_post_1_5_kits_lims_samples( - novaseq_6000_post_1_5_kits_raw_lims_samples: Path, -) -> list[FlowCellSampleBCLConvert]: - return [ - FlowCellSampleBCLConvert.model_validate(sample) - for sample in read_json(novaseq_6000_post_1_5_kits_raw_lims_samples) - ] - - -@pytest.fixture -def novaseq_6000_pre_1_5_kits_lims_samples( - novaseq_6000_pre_1_5_kits_raw_lims_samples: Path, -) -> list[FlowCellSampleBCLConvert]: - return [ - FlowCellSampleBCLConvert.model_validate(sample) - for sample in read_json(novaseq_6000_pre_1_5_kits_raw_lims_samples) - ] - - -@pytest.fixture -def novaseq_x_lims_samples(novaseq_x_raw_lims_samples: Path) -> list[FlowCellSampleBCLConvert]: - return [ - FlowCellSampleBCLConvert.model_validate(sample) - for sample in read_json(novaseq_x_raw_lims_samples) - ] - - @pytest.fixture def hiseq_x_single_index_bcl_convert_lims_samples( hiseq_x_single_index_flow_cell_dir: Path, ) -> list[FlowCellSampleBCLConvert]: - """Return a list of BCLConvert samples from a HiSeqX single index flow cell.""" + """Return a list of BCLConvert samples parsed from LIMS for a HiSeqX single index flow cell.""" path = Path( hiseq_x_single_index_flow_cell_dir, f"HJCFFALXX_bcl_convert_raw{FileExtensions.JSON}" ) @@ -96,7 +28,7 @@ def hiseq_x_single_index_bcl_convert_lims_samples( def hiseq_x_dual_index_bcl_convert_lims_samples( hiseq_x_dual_index_flow_cell_dir: Path, ) -> list[FlowCellSampleBCLConvert]: - """Return a list of BCLConvert samples from a HiSeqX dual index flow cell.""" + """Return a list of BCLConvert samples parsed from LIMS for a HiSeqX dual index flow cell.""" path = Path(hiseq_x_dual_index_flow_cell_dir, f"HL32LCCXY_bcl_convert_raw{FileExtensions.JSON}") return [FlowCellSampleBCLConvert.model_validate(sample) for sample in read_json(path)] @@ -105,7 +37,7 @@ def hiseq_x_dual_index_bcl_convert_lims_samples( def hiseq_2500_dual_index_bcl_convert_lims_samples( hiseq_2500_dual_index_flow_cell_dir: Path, ) -> list[FlowCellSampleBCLConvert]: - """Return a list of BCLConvert samples from a HiSeq2500 dual index flow cell.""" + """Return a list of BCLConvert samples parsed from LIMS for a HiSeq2500 dual index flow cell.""" path = Path(hiseq_2500_dual_index_flow_cell_dir, "HM2LNBCX2_bcl_convert_raw.json") return [FlowCellSampleBCLConvert.model_validate(sample) for sample in read_json(path)] @@ -114,22 +46,55 @@ def hiseq_2500_dual_index_bcl_convert_lims_samples( def hiseq_2500_custom_index_bcl_convert_lims_samples( hiseq_2500_custom_index_flow_cell_dir: Path, ) -> list[FlowCellSampleBCLConvert]: - """Return a list of BCLConvert samples from a HiSeq2500 custom index flow cell.""" + """Return a list of BCLConvert samples parsed from LIMS for a HiSeq2500 custom index flow cell.""" path = Path(hiseq_2500_custom_index_flow_cell_dir, "HGYFNBCX2_bcl_convert_raw.json") return [FlowCellSampleBCLConvert.model_validate(sample) for sample in read_json(path)] @pytest.fixture -def lims_novaseq_samples_raw(lims_novaseq_samples_file: Path) -> list[dict]: - """Return a list of raw flow cell samples.""" - return ReadFile.get_content_from_file( - file_format=FileFormat.JSON, file_path=lims_novaseq_samples_file - ) +def novaseq_6000_pre_1_5_kits_bcl2fastq_lims_samples( + novaseq_6000_pre_1_5_kits_flow_cell_path: Path, +) -> list[FlowCellSampleBcl2Fastq]: + """Return a list of Bcl2Fastq samples parsed from LIMS for a NovaSeq6000 pre 1.5 flow cell.""" + path = Path(novaseq_6000_pre_1_5_kits_flow_cell_path, "HLYWYDSXX_bcl2fastq_raw.json") + return [FlowCellSampleBcl2Fastq.model_validate(sample) for sample in read_json(path)] + + +@pytest.fixture +def novaseq_6000_pre_1_5_kits_bcl_convert_lims_samples( + novaseq_6000_pre_1_5_kits_flow_cell_path: Path, +) -> list[FlowCellSampleBCLConvert]: + """Return a list of BCLConvert samples parsed from LIMS for a NovaSeq6000 pre 1.5 flow cell.""" + path = Path(novaseq_6000_pre_1_5_kits_flow_cell_path, "HLYWYDSXX_bcl_convert_raw.json") + return [FlowCellSampleBCLConvert.model_validate(sample) for sample in read_json(path)] @pytest.fixture -def lims_novaseq_6000_sample_raw(lims_novaseq_6000_samples_file: Path) -> list[dict]: - """Return the list of raw samples from flow cell HVKJCDRXX.""" - return ReadFile.get_content_from_file( - file_format=FileFormat.JSON, file_path=lims_novaseq_6000_samples_file +def novaseq_6000_post_1_5_kits_bcl_convert_lims_samples( + novaseq_6000_post_1_5_kits_flow_cell_path: Path, +) -> list[FlowCellSampleBCLConvert]: + """Return a list of BCLConvert samples parsed from LIMS for a NovaSeq6000 post 1.5 flow cell.""" + path = Path(novaseq_6000_post_1_5_kits_flow_cell_path, "HK33MDRX3_bcl_convert_raw.json") + return [FlowCellSampleBCLConvert.model_validate(sample) for sample in read_json(path)] + + +@pytest.fixture +def novaseq_x_lims_samples(novaseq_x_flow_cell_directory: Path) -> list[FlowCellSampleBCLConvert]: + """Return a list of BCLConvert samples parsed from LIMS for a NovaSeqX flow cell.""" + path = Path(novaseq_x_flow_cell_directory, "22F52TLT3_raw.json") + return [FlowCellSampleBCLConvert.model_validate(sample) for sample in read_json(path)] + + +# Sample sheet creators + + +@pytest.fixture +def bcl_convert_sample_sheet_creator( + bcl_convert_flow_cell: FlowCellDirectoryData, + novaseq_x_lims_samples: list[FlowCellSampleBCLConvert], +) -> SampleSheetCreatorBCLConvert: + """Returns a sample sheet creator for sample sheet v2.""" + return SampleSheetCreatorBCLConvert( + flow_cell=bcl_convert_flow_cell, + lims_samples=novaseq_x_lims_samples, ) diff --git a/tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/HLYWYDSXX_bcl2fastq_raw.json b/tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/HLYWYDSXX_bcl2fastq_raw.json new file mode 100644 index 0000000000..e8384fa508 --- /dev/null +++ b/tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/HLYWYDSXX_bcl2fastq_raw.json @@ -0,0 +1,6398 @@ +[ + { + "lane": 1, + "sample_id": "ACC6217A12", + "index": "CGATAGCAGG-AATGCTACGA", + "index2": "", + "flowcell_id": "HLYWYDSXX", + "sample_ref": "hg19", + "sample_name": "71421170", + "control": "N", + "recipe": "R1", + "operator": "script", + "project": "TEST81" + }, + { + "lane": 1, + "sample_id": "ACC6217A7", + "index": "ACCGACGTGA-CATGACCGTT", + "index2": "", + "flowcell_id": "HLYWYDSXX", + "sample_ref": "hg19", + "sample_name": "60416520", + "control": "N", + "recipe": "R1", + "operator": "script", + "project": "TEST43" + }, + { + "lane": 1, + "sample_id": "ACC6217A16", + "index": "CCGGTTCATG-CAAGACGTCT", + "index2": "", + "flowcell_id": "HLYWYDSXX", + "sample_ref": "hg19", + "sample_name": "46907745", + "control": "N", + "recipe": "R1", + "operator": "script", + "project": "TEST46" + }, + { + "lane": 1, + "sample_id": "ACC6217A1", + "index": "ATTCCACACT-AACAAGACCA", + "index2": "", + "flowcell_id": "HLYWYDSXX", + "sample_ref": "hg19", + "sample_name": "62263198", + "control": "N", + "recipe": "R1", + "operator": "script", + "project": "TEST34" + }, + { + "lane": 1, + "sample_id": "ACC6217A10", + "index": "CGATGAGACT-GCACGACTAA", + "index2": "", + "flowcell_id": "HLYWYDSXX", + "sample_ref": "hg19", + "sample_name": "38773382", + "control": "N", + "recipe": "R1", + "operator": "script", + "project": "TEST17" + }, + { + "lane": 1, + "sample_id": "ACC6217A8", + "index": "AATCTCAGGC-GAGTTAGAGA", + "index2": "", + "flowcell_id": "HLYWYDSXX", + "sample_ref": "hg19", + "sample_name": "22404337", + "control": "N", + "recipe": "R1", + "operator": 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"project": "TEST26" + } +] \ No newline at end of file diff --git a/tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/HLYWYDSXX_raw.json b/tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/HLYWYDSXX_bcl_convert_raw.json similarity index 100% rename from tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/HLYWYDSXX_raw.json rename to tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/HLYWYDSXX_bcl_convert_raw.json diff --git a/tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/README.txt b/tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/README.txt index 83d3b6eaa3..3e2151c17b 100644 --- a/tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/README.txt +++ b/tests/fixtures/apps/demultiplexing/flow_cells/190927_A00689_0069_BHLYWYDSXX/README.txt @@ -2,4 +2,5 @@ Sequencer: NovaSeq6000 Workflow: PairedEnd Indexes: 10, 10 BCL converter: BCLConvert -Kit: Pre 1.5 \ No newline at end of file +Kit: Pre 1.5 +Notes: A sample sheet from this flow cell would NOT have reverse-complemented index 2 (i5) NOR reverse-complemented override cycles (on index 2). \ No newline at end of file diff --git a/tests/fixtures/apps/demultiplexing/flow_cells/230912_A00187_1009_AHK33MDRX3/HK33MDRX3_raw.json b/tests/fixtures/apps/demultiplexing/flow_cells/230912_A00187_1009_AHK33MDRX3/HK33MDRX3_bcl_convert_raw.json similarity index 100% rename from tests/fixtures/apps/demultiplexing/flow_cells/230912_A00187_1009_AHK33MDRX3/HK33MDRX3_raw.json rename to tests/fixtures/apps/demultiplexing/flow_cells/230912_A00187_1009_AHK33MDRX3/HK33MDRX3_bcl_convert_raw.json diff --git a/tests/fixtures/apps/demultiplexing/flow_cells/230912_A00187_1009_AHK33MDRX3/README.txt b/tests/fixtures/apps/demultiplexing/flow_cells/230912_A00187_1009_AHK33MDRX3/README.txt index e457c244a5..3305225ccc 100644 --- a/tests/fixtures/apps/demultiplexing/flow_cells/230912_A00187_1009_AHK33MDRX3/README.txt +++ b/tests/fixtures/apps/demultiplexing/flow_cells/230912_A00187_1009_AHK33MDRX3/README.txt @@ -2,4 +2,5 @@ Sequencer: NovaSeq6000 Workflow: PairedEnd Indexes: 10, 10 BCL converter: BCLConvert -Kit: Post 1.5 \ No newline at end of file +Kit: Post 1.5 +Notes: A sample sheet from this flow cell would have reverse-complemented index 2 (i5) but NOT reverse-complemented override cycles (on index 2). \ No newline at end of file