diff --git a/cg/meta/workflow/nallo.py b/cg/meta/workflow/nallo.py index ec88c2df26..23c4f7234a 100644 --- a/cg/meta/workflow/nallo.py +++ b/cg/meta/workflow/nallo.py @@ -68,7 +68,6 @@ def __init__( self.email: str = config.nallo.slurm.mail_user self.compute_env_base: str = config.nallo.compute_env self.revision: str = config.nallo.revision - self.nextflow_binary_path: str = config.nallo.binary_path @property def sample_sheet_headers(self) -> list[str]: diff --git a/cg/meta/workflow/raredisease.py b/cg/meta/workflow/raredisease.py index 56a6841edf..be8fedce21 100644 --- a/cg/meta/workflow/raredisease.py +++ b/cg/meta/workflow/raredisease.py @@ -69,7 +69,6 @@ def __init__( self.email: str = config.raredisease.slurm.mail_user self.compute_env_base: str = config.raredisease.compute_env self.revision: str = config.raredisease.revision - self.nextflow_binary_path: str = config.raredisease.binary_path @property def sample_sheet_headers(self) -> list[str]: diff --git a/cg/meta/workflow/rnafusion.py b/cg/meta/workflow/rnafusion.py index 75fbf27a68..89d2053780 100644 --- a/cg/meta/workflow/rnafusion.py +++ b/cg/meta/workflow/rnafusion.py @@ -48,7 +48,6 @@ def __init__( self.email: str = config.rnafusion.slurm.mail_user self.compute_env_base: str = config.rnafusion.compute_env self.revision: str = config.rnafusion.revision - self.nextflow_binary_path: str = config.rnafusion.binary_path @property def sample_sheet_headers(self) -> list[str]: diff --git a/cg/meta/workflow/taxprofiler.py b/cg/meta/workflow/taxprofiler.py index 6833f0371e..e87347ddb1 100644 --- a/cg/meta/workflow/taxprofiler.py +++ b/cg/meta/workflow/taxprofiler.py @@ -46,7 +46,6 @@ def __init__( self.tower_workflow: str = config.taxprofiler.tower_workflow self.account: str = config.taxprofiler.slurm.account self.email: str = config.taxprofiler.slurm.mail_user - self.nextflow_binary_path: str = config.taxprofiler.binary_path self.compute_env_base: str = config.taxprofiler.compute_env @property diff --git a/cg/meta/workflow/tomte.py b/cg/meta/workflow/tomte.py index d4044f828f..8f09556418 100644 --- a/cg/meta/workflow/tomte.py +++ b/cg/meta/workflow/tomte.py @@ -46,7 +46,6 @@ def __init__( self.email: str = config.tomte.slurm.mail_user self.compute_env_base: str = config.tomte.compute_env self.revision: str = config.tomte.revision - self.nextflow_binary_path: str = config.tomte.binary_path @property def sample_sheet_headers(self) -> list[str]: diff --git a/cg/models/cg_config.py b/cg/models/cg_config.py index b71e5e6dea..f7acb52624 100644 --- a/cg/models/cg_config.py +++ b/cg/models/cg_config.py @@ -230,102 +230,25 @@ class MipConfig(BaseModel): script: str -class NalloConfig(CommonAppConfig): - binary_path: str | None = None - compute_env: str - conda_binary: str | None = None - conda_env: str - platform: str - params: str - config: str - resources: str - launch_directory: str - workflow_bin_path: str - pre_run_script: str = "" - profile: str - repository: str - revision: str - root: str - slurm: SlurmConfig - tower_workflow: str - +class NextflowConfig(BaseModel): + """Contains the Nextflow parameters (different from pipeline parameters!) + used for running Nextflow pipelines.""" -class RarediseaseConfig(CommonAppConfig): - binary_path: str | None = None compute_env: str - conda_binary: str | None = None + conda_binary: str conda_env: str - platform: str - params: str config: str - resources: str - launch_directory: str - workflow_bin_path: str - pre_run_script: str = "" - profile: str - repository: str - revision: str - root: str - slurm: SlurmConfig - tower_workflow: str - - -class TomteConfig(CommonAppConfig): - binary_path: str | None = None - compute_env: str - conda_binary: str | None = None - conda_env: str - platform: str params: str - config: str - resources: str - workflow_bin_path: str - pre_run_script: str = "" - profile: str - repository: str - revision: str - root: str - slurm: SlurmConfig - tower_workflow: str - - -class RnafusionConfig(CommonAppConfig): - binary_path: str - compute_env: str - conda_binary: str | None = None - conda_env: str platform: str - params: str - config: str - resources: str - launch_directory: str - pre_run_script: str = "" + pre_run_script: str profile: str repository: str - revision: str - root: str - slurm: SlurmConfig - tower_workflow: str - workflow_bin_path: str - - -class TaxprofilerConfig(CommonAppConfig): - binary_path: str - conda_binary: str | None = None - conda_env: str - compute_env: str - platform: str - params: str - config: str resources: str - workflow_bin_path: str - pre_run_script: str = "" - profile: str - repository: str revision: str root: str slurm: SlurmConfig tower_workflow: str + workflow_bin_path: str class MicrosaltConfig(BaseModel): @@ -508,12 +431,12 @@ class CGConfig(BaseModel): mip_rd_dna: MipConfig = Field(None, alias="mip-rd-dna") mip_rd_rna: MipConfig | None = Field(None, alias="mip-rd-rna") mutant: MutantConfig | None = None - nallo: NalloConfig | None = None - raredisease: RarediseaseConfig | None = None - rnafusion: RnafusionConfig | None = None + nallo: NextflowConfig | None = None + raredisease: NextflowConfig | None = None + rnafusion: NextflowConfig | None = None statina: StatinaConfig | None = None - taxprofiler: TaxprofilerConfig | None = None - tomte: TomteConfig | None = None + taxprofiler: NextflowConfig | None = None + tomte: NextflowConfig | None = None # These are meta APIs that gets instantiated in the code meta_apis: dict = {} diff --git a/cg/services/analysis_starter/configurator/implementations/nextflow.py b/cg/services/analysis_starter/configurator/implementations/nextflow.py index 86c8746485..a6438de0c0 100644 --- a/cg/services/analysis_starter/configurator/implementations/nextflow.py +++ b/cg/services/analysis_starter/configurator/implementations/nextflow.py @@ -1,7 +1,7 @@ from pathlib import Path from cg.exc import AnalysisAlreadyCompletedError, MissingConfigFilesError -from cg.models.cg_config import CommonAppConfig +from cg.models.cg_config import NextflowConfig from cg.services.analysis_starter.configurator.configurator import Configurator from cg.services.analysis_starter.configurator.extensions.pipeline_extension import ( PipelineExtension, @@ -25,7 +25,7 @@ def __init__( self, config_file_creator: NextflowConfigFileCreator, params_file_creator: ParamsFileCreator, - pipeline_config: CommonAppConfig, + pipeline_config: NextflowConfig, sample_sheet_creator: SampleSheetCreator, store: Store, pipeline_extension: PipelineExtension = PipelineExtension(), diff --git a/cg/services/analysis_starter/factories/configurator_factory.py b/cg/services/analysis_starter/factories/configurator_factory.py index f2e1aa9498..10264a443e 100644 --- a/cg/services/analysis_starter/factories/configurator_factory.py +++ b/cg/services/analysis_starter/factories/configurator_factory.py @@ -5,7 +5,7 @@ from cg.apps.scout.scoutapi import ScoutAPI from cg.constants import Workflow from cg.meta.workflow.fastq import BalsamicFastqHandler, MicrosaltFastqHandler, MipFastqHandler -from cg.models.cg_config import CGConfig, CommonAppConfig +from cg.models.cg_config import CGConfig, NextflowConfig from cg.services.analysis_starter.configurator.configurator import Configurator from cg.services.analysis_starter.configurator.extensions.nallo import NalloExtension from cg.services.analysis_starter.configurator.extensions.pipeline_extension import ( @@ -75,7 +75,6 @@ class ConfiguratorFactory: - def __init__(self, cg_config: CGConfig): self.cg_config = cg_config self.housekeeper_api: HousekeeperAPI = cg_config.housekeeper_api @@ -118,7 +117,7 @@ def _get_nextflow_configurator(self, workflow: Workflow) -> NextflowConfigurator ) def _get_nextflow_config_file_creator(self, workflow: Workflow) -> NextflowConfigFileCreator: - pipeline_config: CommonAppConfig = self._get_pipeline_config(workflow) + pipeline_config: NextflowConfig = self._get_pipeline_config(workflow) return NextflowConfigFileCreator( account=pipeline_config.slurm.account, platform=pipeline_config.platform, @@ -147,7 +146,7 @@ def _get_params_file_creator(self, workflow: Workflow) -> ParamsFileCreator: case _: raise NotImplementedError(f"There is no params file creator for {workflow}") - def _get_pipeline_config(self, workflow: Workflow) -> CommonAppConfig: + def _get_pipeline_config(self, workflow: Workflow) -> NextflowConfig: return getattr(self.cg_config, workflow) def _get_sample_sheet_creator(self, workflow: Workflow) -> SampleSheetCreator: diff --git a/tests/conftest.py b/tests/conftest.py index 231e1f5d22..b9a7b4cb97 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2148,20 +2148,16 @@ def context_config( "root": str(mip_dir), }, "nallo": { - "binary_path": nextflow_binary.as_posix(), "compute_env": "nf_tower_compute_env", "conda_binary": conda_binary.as_posix(), "conda_env": "S_nallo", - "platform": str(nf_analysis_platform_config_path), - "params": str(nf_analysis_pipeline_params_path), "config": str(nf_analysis_pipeline_config_path), - "resources": str(nf_analysis_pipeline_resource_optimisation_path), - "launch_directory": Path("path", "to", "launchdir").as_posix(), - "workflow_bin_path": Path("workflow", "path").as_posix(), + "params": str(nf_analysis_pipeline_params_path), + "platform": str(nf_analysis_platform_config_path), "pre_run_script": "", "profile": "myprofile", "repository": "https://some_url", - "references": Path("path", "to", "references").as_posix(), + "resources": str(nf_analysis_pipeline_resource_optimisation_path), "revision": "2.2.0", "root": str(nallo_dir), "slurm": { @@ -2169,21 +2165,20 @@ def context_config( "mail_user": email_address, }, "tower_workflow": "nallo", + "workflow_bin_path": Path("workflow", "path").as_posix(), }, "raredisease": { - "binary_path": nextflow_binary.as_posix(), "compute_env": "nf_tower_compute_env", "conda_binary": conda_binary.as_posix(), "conda_env": "S_raredisease", - "platform": str(nf_analysis_platform_config_path), - "params": str(nf_analysis_pipeline_params_path), "config": str(nf_analysis_pipeline_config_path), - "resources": str(nf_analysis_pipeline_resource_optimisation_path), - "launch_directory": Path("path", "to", "launchdir").as_posix(), - "workflow_bin_path": Path("workflow", "path").as_posix(), + "params": str(nf_analysis_pipeline_params_path), + "platform": str(nf_analysis_platform_config_path), + "pre_run_script": "", "profile": "myprofile", "references": Path("path", "to", "references").as_posix(), "repository": "https://some_url", + "resources": str(nf_analysis_pipeline_resource_optimisation_path), "revision": "2.2.0", "root": str(raredisease_dir), "slurm": { @@ -2191,21 +2186,20 @@ def context_config( "mail_user": email_address, }, "tower_workflow": "raredisease", + "workflow_bin_path": Path("workflow", "path").as_posix(), }, "tomte": { - "binary_path": nextflow_binary.as_posix(), "compute_env": "nf_tower_compute_env", "conda_binary": conda_binary.as_posix(), "conda_env": "S_tomte", - "platform": str(nf_analysis_platform_config_path), - "params": str(nf_analysis_pipeline_params_path), "config": str(nf_analysis_pipeline_config_path), - "resources": str(nf_analysis_pipeline_resource_optimisation_path), - "workflow_bin_path": Path("workflow", "path").as_posix(), + "params": str(nf_analysis_pipeline_params_path), + "platform": str(nf_analysis_platform_config_path), "pre_run_script": "", "profile": "myprofile", - "repository": "https://some_url", "references": Path("path", "to", "references").as_posix(), + "repository": "https://some_url", + "resources": str(nf_analysis_pipeline_resource_optimisation_path), "revision": "2.2.0", "root": str(tomte_dir), "slurm": { @@ -2213,22 +2207,20 @@ def context_config( "mail_user": email_address, }, "tower_workflow": "tomte", + "workflow_bin_path": Path("workflow", "path").as_posix(), }, "rnafusion": { - "binary_path": nextflow_binary.as_posix(), "compute_env": "nf_tower_compute_env", "conda_binary": conda_binary.as_posix(), "conda_env": "S_RNAFUSION", - "platform": str(nf_analysis_platform_config_path), - "params": str(nf_analysis_pipeline_params_path), "config": str(nf_analysis_pipeline_config_path), - "resources": str(nf_analysis_pipeline_resource_optimisation_path), - "launch_directory": Path("path", "to", "launchdir").as_posix(), - "workflow_bin_path": Path("workflow", "path").as_posix(), + "params": str(nf_analysis_pipeline_params_path), + "platform": str(nf_analysis_platform_config_path), "pre_run_script": "", "profile": "myprofile", "references": Path("path", "to", "references").as_posix(), "repository": "https://some_url", + "resources": str(nf_analysis_pipeline_resource_optimisation_path), "revision": "2.2.0", "root": str(rnafusion_dir), "slurm": { @@ -2236,30 +2228,29 @@ def context_config( "mail_user": "test.rnafusion.email@scilifelab.se", }, "tower_workflow": "rnafusion", + "workflow_bin_path": Path("workflow", "path").as_posix(), }, "pigz": {"binary_path": "/bin/pigz"}, "pdc": {"binary_path": "/bin/dsmc"}, "taxprofiler": { - "binary_path": nextflow_binary.as_posix(), "compute_env": "nf_tower_compute_env", - "root": str(taxprofiler_dir), "conda_binary": conda_binary.as_posix(), "conda_env": "S_taxprofiler", - "platform": str(nf_analysis_platform_config_path), - "params": str(nf_analysis_pipeline_params_path), "config": str(nf_analysis_pipeline_config_path), - "resources": str(nf_analysis_pipeline_resource_optimisation_path), - "launch_directory": Path("path", "to", "launchdir").as_posix(), - "workflow_bin_path": Path("workflow", "path").as_posix(), + "params": str(nf_analysis_pipeline_params_path), + "platform": str(nf_analysis_platform_config_path), "pre_run_script": "", "profile": "myprofile", "repository": "https://some_url", + "resources": str(nf_analysis_pipeline_resource_optimisation_path), "revision": "2.2.0", + "root": str(taxprofiler_dir), "slurm": { "account": "development", "mail_user": "taxprofiler.email@scilifelab.se", }, "tower_workflow": "taxprofiler", + "workflow_bin_path": Path("workflow", "path").as_posix(), }, "scout": { "binary_path": "bin/scout", diff --git a/tests/fixture_plugins/analysis_starter/configurator_fixtures.py b/tests/fixture_plugins/analysis_starter/configurator_fixtures.py index 24409ad4a8..e07df4ead2 100644 --- a/tests/fixture_plugins/analysis_starter/configurator_fixtures.py +++ b/tests/fixture_plugins/analysis_starter/configurator_fixtures.py @@ -4,15 +4,7 @@ from cg.apps.lims import LimsAPI from cg.meta.workflow.fastq import BalsamicFastqHandler, MicrosaltFastqHandler -from cg.models.cg_config import ( - BalsamicConfig, - CGConfig, - NalloConfig, - RarediseaseConfig, - RnafusionConfig, - TaxprofilerConfig, - TomteConfig, -) +from cg.models.cg_config import BalsamicConfig, CGConfig, NextflowConfig from cg.services.analysis_starter.configurator.extensions.tomte_extension import TomteExtension from cg.services.analysis_starter.configurator.file_creators.balsamic_config import ( BalsamicConfigFileCreator, @@ -93,7 +85,7 @@ def microsalt_configurator( @pytest.fixture def nallo_configurator( - mock_store_for_nallo_file_creators: Store, nallo_config_object: NalloConfig + mock_store_for_nallo_file_creators: Store, nallo_config_object: NextflowConfig ) -> NextflowConfigurator: return NextflowConfigurator( store=mock_store_for_nallo_file_creators, @@ -108,7 +100,7 @@ def nallo_configurator( @pytest.fixture def raredisease_configurator( mock_store_for_raredisease_file_creators: Store, - raredisease_config_object: RarediseaseConfig, + raredisease_config_object: NextflowConfig, ) -> NextflowConfigurator: return NextflowConfigurator( store=mock_store_for_raredisease_file_creators, @@ -123,7 +115,7 @@ def raredisease_configurator( @pytest.fixture def rnafusion_configurator( mock_store_for_rnafusion_file_creators: Store, - rnafusion_config_object: RnafusionConfig, + rnafusion_config_object: NextflowConfig, ) -> NextflowConfigurator: return NextflowConfigurator( store=mock_store_for_rnafusion_file_creators, @@ -138,7 +130,7 @@ def rnafusion_configurator( @pytest.fixture def taxprofiler_configurator( mock_store_for_taxprofiler_file_creators: Store, - taxprofiler_config_object: TaxprofilerConfig, + taxprofiler_config_object: NextflowConfig, ) -> NextflowConfigurator: return NextflowConfigurator( store=mock_store_for_taxprofiler_file_creators, @@ -153,7 +145,7 @@ def taxprofiler_configurator( @pytest.fixture def tomte_configurator( mock_store_for_tomte_file_creators: Store, - tomte_config_object: TomteConfig, + tomte_config_object: NextflowConfig, ) -> NextflowConfigurator: return NextflowConfigurator( store=mock_store_for_tomte_file_creators, diff --git a/tests/fixture_plugins/analysis_starter/pipeline_config_fixtures.py b/tests/fixture_plugins/analysis_starter/pipeline_config_fixtures.py index c940d4500a..3216e363d7 100644 --- a/tests/fixture_plugins/analysis_starter/pipeline_config_fixtures.py +++ b/tests/fixture_plugins/analysis_starter/pipeline_config_fixtures.py @@ -5,21 +5,11 @@ from cg.constants import Workflow from cg.constants.observations import BalsamicObservationPanel -from cg.models.cg_config import ( - BalsamicConfig, - LoqusDBDumpFiles, - NalloConfig, - RarediseaseConfig, - RnafusionConfig, - SlurmConfig, - TaxprofilerConfig, - TomteConfig, -) +from cg.models.cg_config import BalsamicConfig, LoqusDBDumpFiles, NextflowConfig, SlurmConfig @pytest.fixture def get_nextflow_config_dict( - nextflow_binary: Path, nextflow_root: str, conda_binary: Path, nf_analysis_platform_config_path: Path, @@ -39,19 +29,16 @@ def get_nextflow_config_dict( def _make_dict(workflow: str) -> dict: return { - "binary_path": nextflow_binary.as_posix(), "compute_env": "nf_tower_compute_env", "conda_binary": conda_binary.as_posix(), "conda_env": f"S_{workflow}", - "platform": str(nf_analysis_platform_config_path), - "params": str(nf_analysis_pipeline_params_path), "config": str(nf_analysis_pipeline_config_path), - "resources": str(nf_analysis_pipeline_resource_optimisation_path), - "launch_directory": Path("path", "to", "launchdir").as_posix(), - "workflow_bin_path": Path("workflow", "path").as_posix(), + "params": str(nf_analysis_pipeline_params_path), + "platform": str(nf_analysis_platform_config_path), + "pre_run_script": "", "profile": "myprofile", - "references": Path("path", "to", "references").as_posix(), "repository": nextflow_repository, + "resources": str(nf_analysis_pipeline_resource_optimisation_path), "revision": nextflow_pipeline_revision, "root": nextflow_root, "slurm": { @@ -59,6 +46,7 @@ def _make_dict(workflow: str) -> dict: "mail_user": email_address, }, "tower_workflow": workflow, + "workflow_bin_path": Path("workflow", "path").as_posix(), } return _make_dict @@ -113,30 +101,30 @@ def cg_balsamic_config(tmp_path) -> BalsamicConfig: @pytest.fixture -def nallo_config_object(get_nextflow_config_dict: Callable) -> NalloConfig: +def nallo_config_object(get_nextflow_config_dict: Callable) -> NextflowConfig: config: dict = get_nextflow_config_dict(workflow=Workflow.NALLO) - return NalloConfig(**config) + return NextflowConfig(**config) @pytest.fixture -def raredisease_config_object(get_nextflow_config_dict: Callable) -> RarediseaseConfig: +def raredisease_config_object(get_nextflow_config_dict: Callable) -> NextflowConfig: config: dict = get_nextflow_config_dict(workflow=Workflow.RAREDISEASE) - return RarediseaseConfig(**config) + return NextflowConfig(**config) @pytest.fixture -def rnafusion_config_object(get_nextflow_config_dict: Callable) -> RnafusionConfig: +def rnafusion_config_object(get_nextflow_config_dict: Callable) -> NextflowConfig: config: dict = get_nextflow_config_dict(workflow=Workflow.RNAFUSION) - return RnafusionConfig(**config) + return NextflowConfig(**config) @pytest.fixture -def taxprofiler_config_object(get_nextflow_config_dict: Callable) -> TaxprofilerConfig: +def taxprofiler_config_object(get_nextflow_config_dict: Callable) -> NextflowConfig: config: dict = get_nextflow_config_dict(workflow=Workflow.TAXPROFILER) - return TaxprofilerConfig(**config) + return NextflowConfig(**config) @pytest.fixture -def tomte_config_object(get_nextflow_config_dict: Callable) -> TomteConfig: +def tomte_config_object(get_nextflow_config_dict: Callable) -> NextflowConfig: config: dict = get_nextflow_config_dict(workflow=Workflow.TOMTE) - return TomteConfig(**config) + return NextflowConfig(**config) diff --git a/tests/integration/config/cg-test.yaml b/tests/integration/config/cg-test.yaml index 2535080167..3cd17f1d58 100644 --- a/tests/integration/config/cg-test.yaml +++ b/tests/integration/config/cg-test.yaml @@ -139,11 +139,12 @@ mutacc-auto: nallo: compute_env: nallo_compute_env + conda_binary: "conda_binary" conda_env: nallo_conda_env config: {test_root_dir}/nallo_config.config - launch_directory: {test_root_dir}/nallo_launch_directory params: {test_root_dir}/nallo_params.yaml platform: {test_root_dir}/platform.config + pre_run_script: "pre_run_script.sh" profile: nallo_profile resources: {test_root_dir}/nallo_resources.config repository: nallo_repository diff --git a/tests/services/analysis_starter/test_analysis_starter_factory.py b/tests/services/analysis_starter/test_analysis_starter_factory.py index 07c67619e5..1559bf3e0e 100644 --- a/tests/services/analysis_starter/test_analysis_starter_factory.py +++ b/tests/services/analysis_starter/test_analysis_starter_factory.py @@ -11,13 +11,9 @@ CGConfig, IlluminaConfig, MipConfig, - NalloConfig, - RarediseaseConfig, - RnafusionConfig, + NextflowConfig, RunInstruments, SeqeraPlatformConfig, - TaxprofilerConfig, - TomteConfig, ) from cg.services.analysis_starter.analysis_starter import AnalysisStarter from cg.services.analysis_starter.configurator.implementations.balsamic import BalsamicConfigurator @@ -130,11 +126,11 @@ def test_analysis_starter_factory_mip_dna(): ) def test_get_analysis_starter_for_workflow_nextflow_fastq( nextflow_root: str, - raredisease_config_object: RarediseaseConfig, - rnafusion_config_object: RnafusionConfig, + raredisease_config_object: NextflowConfig, + rnafusion_config_object: NextflowConfig, seqera_platform_config: SeqeraPlatformConfig, - taxprofiler_config_object: TaxprofilerConfig, - tomte_config_object: TomteConfig, + taxprofiler_config_object: NextflowConfig, + tomte_config_object: NextflowConfig, workflow: Workflow, mocker: MockerFixture, ): @@ -222,7 +218,7 @@ def test_get_analysis_starter_for_workflow_nextflow_fastq( def test_get_analysis_starter_for_workflow_nallo( - nallo_config_object: NalloConfig, + nallo_config_object: NextflowConfig, mocker: MockerFixture, ): """Test that the AnalysisStarterFactory creates a Nallo AnalysisStarter correctly.""" diff --git a/tests/services/analysis_starter/test_nextflow_configurator.py b/tests/services/analysis_starter/test_nextflow_configurator.py index 9e7b7b9ad5..84dd537671 100644 --- a/tests/services/analysis_starter/test_nextflow_configurator.py +++ b/tests/services/analysis_starter/test_nextflow_configurator.py @@ -10,14 +10,7 @@ from cg.constants import Workflow from cg.constants.priority import SlurmQos from cg.exc import AnalysisAlreadyCompletedError, MissingConfigFilesError -from cg.models.cg_config import ( - CommonAppConfig, - NalloConfig, - RarediseaseConfig, - RnafusionConfig, - TaxprofilerConfig, - TomteConfig, -) +from cg.models.cg_config import CommonAppConfig, NextflowConfig from cg.services.analysis_starter.configurator.extensions.pipeline_extension import ( PipelineExtension, ) @@ -110,7 +103,7 @@ def test_get_config_missing_required_files(mocker: MockerFixture): # GIVEN a raredisease config pipeline_config = create_autospec( - RarediseaseConfig, + NextflowConfig, root="/root", repository="https://repo.scilifelab.se", revision="rev123", @@ -279,31 +272,31 @@ def test_get_case_config_none_flags( ( Workflow.NALLO, NalloParamsFileCreator, - NalloConfig, + NextflowConfig, NalloSampleSheetCreator, ), ( Workflow.RAREDISEASE, RarediseaseParamsFileCreator, - RarediseaseConfig, + NextflowConfig, RarediseaseSampleSheetCreator, ), ( Workflow.RNAFUSION, RNAFusionParamsFileCreator, - RnafusionConfig, + NextflowConfig, RNAFusionSampleSheetCreator, ), ( Workflow.TAXPROFILER, TaxprofilerParamsFileCreator, - TaxprofilerConfig, + NextflowConfig, TaxprofilerSampleSheetCreator, ), ( Workflow.TOMTE, TomteParamsFileCreator, - TomteConfig, + NextflowConfig, TomteSampleSheetCreator, ), ],