RAREDISEASE: add store, store available and store housekeeper commands (

#3128)

### Added

- store, store-available and store-housekeeper commands for raredisease with template file bundle for deliverables

### Changed

- 

### Fixed

-

cg/cli/workflow/nf_analysis.py

@@ -313,14 +313,10 @@ def store_available(context: click.Context, dry_run: bool) -> None:
 
     analysis_api: NfAnalysisAPI = context.obj.meta_apis[MetaApis.ANALYSIS_API]
 
-    exit_code: int = EXIT_SUCCESS
-
     for case in analysis_api.get_cases_to_store():
         LOG.info(f"Storing deliverables for {case.internal_id}")
         try:
             analysis_api.store(case_id=case.internal_id, dry_run=dry_run)
         except Exception as error:
             LOG.error(f"Error storing {case.internal_id}: {repr(error)}")
-            exit_code: int = EXIT_FAIL
-    if exit_code:
-        raise click.Abort
+            raise click.Abort

cg/cli/workflow/raredisease/base.py

@@ -9,9 +9,13 @@
 from cg.cli.workflow.nf_analysis import (
     config_case,
     metrics_deliver,
+    report_deliver,
     run,
     start,
     start_available,
+    store,
+    store_available,
+    store_housekeeper,
 )
 from cg.constants.cli_options import DRY_RUN
 from cg.constants.constants import MetaApis
@@ -33,9 +37,13 @@ def raredisease(context: click.Context) -> None:
 raredisease.add_command(metrics_deliver)
 raredisease.add_command(resolve_compression)
 raredisease.add_command(config_case)
+raredisease.add_command(report_deliver)
 raredisease.add_command(run)
 raredisease.add_command(start)
 raredisease.add_command(start_available)
+raredisease.add_command(store)
+raredisease.add_command(store_available)
+raredisease.add_command(store_housekeeper)
 
 
 @raredisease.command("panel")

cg/constants/nextflow.py

@@ -1,6 +1,7 @@
 """Nextflow related constants."""
 
 from enum import IntEnum
+from cg.constants import Workflow
 
 NFX_WORK_DIR = "work"
 NFX_SAMPLE_HEADER = "sample"
@@ -12,6 +13,12 @@
 NXF_PID_FILE_ENV = "NXF_PID_FILE"
 NXF_JVM_ARGS_ENV = "NXF_JVM_ARGS"
 JAVA_MEMORY_HEADJOB = "-Xmx5g"
+NEXTFLOW_WORKFLOWS: list = [
+    Workflow.RAREDISEASE,
+    Workflow.RNAFUSION,
+    Workflow.TAXPROFILER,
+    Workflow.TOMTE,
+]
 
 
 class SlurmHeadJobDefaults(IntEnum):

cg/meta/workflow/nf_analysis.py

@@ -544,15 +544,16 @@ def run_analysis(
 
     def get_deliverables_template_content(self) -> list[dict[str, str]]:
         """Return deliverables file template content."""
+        LOG.debug("Getting deliverables file template content")
         return ReadFile.get_content_from_file(
             file_format=FileFormat.YAML,
             file_path=self.get_bundle_filenames_path(),
         )
 
     @staticmethod
-    def get_bundle_filenames_path() -> Path | None:
+    def get_bundle_filenames_path() -> Path:
         """Return bundle filenames path."""
-        return None
+        raise NotImplementedError
 
     @staticmethod
     def get_formatted_file_deliverable(
@@ -607,7 +608,6 @@ def get_deliverables_for_case(self, case_id: str) -> WorkflowDeliverables:
                 sample=sample, case_id=case_id, template=deliverable_template
             )
             files.extend(bundle for bundle in bundles_per_sample if bundle not in files)
-
         return WorkflowDeliverables(files=files)
 
     def get_multiqc_json_path(self, case_id: str) -> Path:
@@ -766,10 +766,10 @@ def report_deliver(self, case_id: str, dry_run: bool = False, force: bool = Fals
         if dry_run:
             LOG.info(f"Dry-run: Would have created delivery files for case {case_id}")
             return
-        workflow_content: WorkflowDeliverables = self.get_deliverables_for_case(case_id)
+        workflow_content: WorkflowDeliverables = self.get_deliverables_for_case(case_id=case_id)
         self.write_deliverables_file(
             deliverables_content=workflow_content.dict(),
-            file_path=self.get_deliverables_file_path(case_id),
+            file_path=self.get_deliverables_file_path(case_id=case_id),
         )
         LOG.info(
             f"Writing deliverables file in {self.get_deliverables_file_path(case_id=case_id).as_posix()}"

cg/meta/workflow/raredisease.py

@@ -16,6 +16,7 @@
     RarediseaseSampleSheetEntry,
     RarediseaseSampleSheetHeaders,
 )
+from cg.resources import RAREDISEASE_BUNDLE_FILENAMES_PATH
 from cg.store.models import CaseSample, Sample
 
 LOG = logging.getLogger(__name__)
@@ -116,6 +117,11 @@ def get_sex_code(sex: str) -> int:
             raise ValueError(f"{sex} is not a valid sex")
         return code
 
+    @staticmethod
+    def get_bundle_filenames_path() -> Path:
+        """Return Raredisease bundle filenames path."""
+        return RAREDISEASE_BUNDLE_FILENAMES_PATH
+
     @property
     def root(self) -> str:
         return self.config.raredisease.root

cg/resources/__init__.py

@@ -4,6 +4,10 @@
 
 from cg.constants import FileExtensions
 
+RAREDISEASE_BUNDLE_FILENAMES: str = (
+    Path("resources", "raredisease_bundle_filenames").with_suffix(FileExtensions.YAML).as_posix()
+)
+
 RNAFUSION_BUNDLE_FILENAMES: str = (
     Path("resources", "rnafusion_bundle_filenames").with_suffix(FileExtensions.YAML).as_posix()
 )
@@ -16,6 +20,10 @@
     Path("resources", "tomte_bundle_filenames").with_suffix(FileExtensions.YAML).as_posix()
 )
 
+RAREDISEASE_BUNDLE_FILENAMES_PATH = Path(
+    pkg_resources.resource_filename("cg", RAREDISEASE_BUNDLE_FILENAMES)
+)
+
 RNAFUSION_BUNDLE_FILENAMES_PATH: Path = Path(
     pkg_resources.resource_filename("cg", RNAFUSION_BUNDLE_FILENAMES)
 )