Merge branch 'master' into rename-order-status-column

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 63.0.10
+current_version = 63.0.13
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "63.0.10"
+__version__ = "63.0.13"

cg/models/orders/constants.py

@@ -13,6 +13,7 @@ class OrderType(StrEnum):
     MICROSALT: str = Workflow.MICROSALT
     MIP_DNA: str = Workflow.MIP_DNA
     MIP_RNA: str = Workflow.MIP_RNA
+    PACBIO_LONG_READ = "pacbio-long-read"
     RML: str = "rml"
     RNAFUSION: str = Workflow.RNAFUSION
     SARS_COV_2: str = "sars-cov-2"

cg/services/run_devices/abstract_classes.py

@@ -4,6 +4,7 @@
 from pathlib import Path
 
 from cg.services.run_devices.abstract_models import PostProcessingDTOs, RunData, RunMetrics
+from cg.services.run_devices.constants import POST_PROCESSING_COMPLETED
 
 
 class RunDataGenerator(ABC):
@@ -73,6 +74,12 @@ def post_process(self, run_name: str, dry_run: bool = False):
         """Store sequencing metrics in StatusDB and relevant files in Housekeeper."""
         pass
 
+    @staticmethod
+    def _touch_post_processing_complete(run_data: RunData) -> None:
+        """Touch the post-processing complete file."""
+        processing_complete_file = Path(run_data.full_path, POST_PROCESSING_COMPLETED)
+        processing_complete_file.touch()
+
 
 class FileTransferValidationService(ABC):
     """Abstract class that validates file transfers for instrument runs from NAS to Hasta."""

cg/services/run_devices/constants.py

@@ -0,0 +1 @@
+POST_PROCESSING_COMPLETED = "post_processing_completed"

cg/services/run_devices/pacbio/post_processing_service.py

@@ -1,6 +1,8 @@
 import logging
+from pathlib import Path
 
 from cg.services.run_devices.abstract_classes import PostProcessingService
+from cg.services.run_devices.constants import POST_PROCESSING_COMPLETED
 from cg.services.run_devices.error_handler import handle_post_processing_errors
 from cg.services.run_devices.exc import (
     PostProcessingError,
@@ -52,3 +54,4 @@ def post_process(self, run_name: str, dry_run: bool = False) -> None:
         )
         self.store_service.store_post_processing_data(run_data=run_data, dry_run=dry_run)
         self.hk_service.store_files_in_housekeeper(run_data=run_data, dry_run=dry_run)
+        self._touch_post_processing_complete(run_data=run_data)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "63.0.10"
+version = "63.0.13"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"