Add parent model for nextflow configs

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]:

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]:

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]:

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

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]:

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 = {}

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(),

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:

tests/conftest.py

@@ -2148,118 +2148,109 @@ 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": {
                 "account": "development",
                 "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": {
                 "account": "development",
                 "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": {
                 "account": "development",
                 "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": {
                 "account": "development",
                 "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",