fix: support configured nextflow directories

cg/apps/demultiplex/sample_sheet/override_cycles_validator.py

@@ -41,7 +41,7 @@ def set_attributes_from_sample(self, sample: dict[str, str]) -> None:
     def _is_index_cycle_value_following_pattern(
         pattern: str, index_cycle: str, run_cycles: int, index_sequence: str
     ) -> bool:
-        """
+        r"""
         Returns whether an index cycle string is following a valid cycle regex pattern and has
         consistent values. Valid patterns are 'I(\d+)N(\d+)' and 'N(\d+)I(\d+)'. Having consistent
         values means that the sum of the number of index characters (I) and the number of ignored

cg/models/cg_config.py

@@ -257,6 +257,7 @@ class MipConfig(BaseModel):
 
 class NalloConfig(CommonAppConfig):
     binary_path: str | None = None
+    case_run_directory: str | None = None
     conda_binary: str | None = None
     conda_env: str
     config: str
@@ -277,6 +278,7 @@ class NalloConfig(CommonAppConfig):
     slurm: SlurmConfig
     tower_workflow: str
     variant_catalog: Path
+    work_dir: str | None = None
     workflow_bin_path: str
 
 
@@ -299,6 +301,7 @@ class GCNVCallerFiles(BaseModel):
 
 class RarediseaseConfig(CommonAppConfig):
     binary_path: str | None = None
+    case_run_directory: str | None = None
     conda_binary: str | None = None
     conda_env: str
     config: str
@@ -323,11 +326,13 @@ class RarediseaseConfig(CommonAppConfig):
     tower_workflow: str
     variant_catalog: Path
     verifybamid_svd: VerifybamidSvdFilesSet
+    work_dir: str | None = None
     workflow_bin_path: str
 
 
 class TomteConfig(CommonAppConfig):
     binary_path: str | None = None
+    case_run_directory: str | None = None
     conda_binary: str | None = None
     conda_env: str
     config: str
@@ -342,11 +347,13 @@ class TomteConfig(CommonAppConfig):
     root: str
     slurm: SlurmConfig
     tower_workflow: str
+    work_dir: str | None = None
     workflow_bin_path: str
 
 
 class RnafusionConfig(CommonAppConfig):
     binary_path: str
+    case_run_directory: str | None = None
     conda_binary: str | None = None
     conda_env: str
     config: str
@@ -362,11 +369,13 @@ class RnafusionConfig(CommonAppConfig):
     root: str
     slurm: SlurmConfig
     tower_workflow: str
+    work_dir: str | None = None
     workflow_bin_path: str
 
 
 class TaxprofilerConfig(CommonAppConfig):
     binary_path: str
+    case_run_directory: str | None = None
     conda_binary: str | None = None
     conda_env: str
     config: str
@@ -381,6 +390,7 @@ class TaxprofilerConfig(CommonAppConfig):
     root: str
     slurm: SlurmConfig
     tower_workflow: str
+    work_dir: str | None = None
     workflow_bin_path: str
 
 

cg/services/analysis_starter/configurator/implementations/nextflow.py

@@ -31,6 +31,8 @@ def __init__(
         pipeline_extension: PipelineExtension = PipelineExtension(),
     ):
         self.root_dir: str = pipeline_config.root
+        self.case_run_directory: str | None = getattr(pipeline_config, "case_run_directory", None)
+        self.work_dir: str | None = getattr(pipeline_config, "work_dir", None)
         self.pipeline_repository = pipeline_config.repository
         self.pipeline_revision = pipeline_config.revision
         self.config_profiles = [pipeline_config.profile]
@@ -115,15 +117,18 @@ def _get_sample_sheet_path(self, case_id: str) -> Path:
 
     def _get_case_run_directory(self, case_id: str) -> Path:
         """Path to case working directory."""
-        return Path(self.root_dir, case_id)
+        run_directory: str = self.case_run_directory or self.root_dir
+        return Path(run_directory, case_id)
 
     def _create_case_directory(self, case_id: str) -> None:
         """Create case working directory."""
         case_path: Path = self._get_case_run_directory(case_id=case_id)
         case_path.mkdir(parents=True, exist_ok=True)
 
     def _get_work_dir(self, case_id: str) -> Path:
-        return Path(self.root_dir, case_id, "work")
+        if self.work_dir:
+            return Path(self.work_dir, case_id)
+        return Path(self._get_case_run_directory(case_id=case_id), "work")
 
     def _ensure_required_config_files_exist(self, config: NextflowCaseConfig) -> None:
         """

tests/services/analysis_starter/test_nextflow_configurator.py

@@ -1,5 +1,6 @@
 from datetime import datetime
 from pathlib import Path
+from types import SimpleNamespace
 from typing import Callable, cast
 from unittest.mock import Mock, create_autospec
 
@@ -105,6 +106,50 @@ def test_get_config(
     )
 
 
+def test_get_config_uses_configured_case_and_work_directories(
+    nextflow_case_id: str,
+    mocker: MockerFixture,
+):
+    pipeline_config = SimpleNamespace(
+        root="/root",
+        case_run_directory="/launch/raredisease",
+        work_dir="/work/raredisease",
+        repository="https://repo.scilifelab.se",
+        revision="rev123",
+        profile="profile",
+        pre_run_script="some_script.sh",
+    )
+    store_mock = create_autospec(Store)
+    store_mock.get_case_workflow = Mock(return_value=Workflow.RAREDISEASE)
+    store_mock.get_case_priority = Mock(return_value=SlurmQos.NORMAL)
+    pipeline_extension = create_autospec(PipelineExtension)
+    configurator = NextflowConfigurator(
+        config_file_creator=create_autospec(NextflowConfigFileCreator),
+        params_file_creator=create_autospec(RarediseaseParamsFileCreator),
+        pipeline_config=pipeline_config,
+        sample_sheet_creator=create_autospec(RarediseaseSampleSheetCreator),
+        store=store_mock,
+        pipeline_extension=pipeline_extension,
+    )
+    mocker.patch.object(Path, "exists", return_value=True)
+
+    case_config = configurator.get_config(case_id=nextflow_case_id)
+
+    expected_case_directory = Path("/launch/raredisease", nextflow_case_id)
+    assert (
+        case_config.nextflow_config_file
+        == Path(expected_case_directory, f"{nextflow_case_id}_nextflow_config.json").as_posix()
+    )
+    assert (
+        case_config.params_file
+        == Path(expected_case_directory, f"{nextflow_case_id}_params_file.yaml").as_posix()
+    )
+    assert case_config.work_dir == Path("/work/raredisease", nextflow_case_id).as_posix()
+    cast(Mock, pipeline_extension.do_required_files_exist).assert_called_once_with(
+        case_run_directory=expected_case_directory
+    )
+
+
 def test_get_config_missing_required_files(mocker: MockerFixture):
     # GIVEN a nextflow configurator