Move pre-processing tasks from process to 'pre_process' method and …

…update accordingly

lib/realms/smartseq3/ss3_project.py

@@ -152,6 +152,14 @@ async def launch(self):
         if not self.samples:
             logging.warning("No samples found for processing. Returning...")
             return
+
+        # Pre-process samples
+        pre_tasks = [sample.pre_process() for sample in self.samples]
+        await asyncio.gather(*pre_tasks)
+
+        # NOTE: Could control whether to proceed with processing based on config or parameters
+
+        # Process samples
         tasks = [sample.process() for sample in self.samples]
         logging.debug(f"Sample tasks created. Waiting for completion...: {tasks}")
         await asyncio.gather(*tasks)

lib/realms/smartseq3/ss3_sample.py

@@ -85,11 +85,9 @@ def status(self):
     def status(self, value):
         self._status = value
 
-    async def process(self):
-        """
-        Process the sample by collecting metadata, creating YAML files, generating Slurm scripts, and submitting jobs.
-        """
-        logging.info(f"Processing sample {self.id}")
+    async def pre_process(self):
+        """Pre-process the sample by collecting metadata and creating YAML files."""
+        logging.info(f"Pre-processing sample {self.id}")
         yaml_metadata = self._collect_yaml_metadata()
         if not yaml_metadata:
             logging.warning(f"Metadata missing for sample {self.id}")
@@ -115,22 +113,16 @@ async def process(self):
         ):
             logging.error(f"Failed to create Slurm script for sample {self.id}.")
             return None
+        else:
+            logging.debug(f"Slurm script created for sample {self.id}")
 
-        # Submit the job
-        logging.debug("Slurm script created. Submitting job")
+    async def process(self):
+        """Process the sample by submitting its job."""
+        logging.debug("Submitting job for sample {self.id}")
         self.job_id = await self.sjob_manager.submit_job(
             self.file_handler.slurm_script_path
         )
 
-        # if self.job_id:
-        #     logging.debug(f"[{self.id}] Job submitted with ID: {self.job_id}")
-
-        #     asyncio.create_task(self.sjob_manager.monitor_job(self.job_id, self))
-        #     logging.debug(f"[{self.id}] Job {self.job_id} submitted for monitoring.")
-        # else:
-        #     logging.error(f"[{self.id}] Failed to submit job.")
-        #     return None
-
         if self.job_id:
             logging.debug(f"[{self.id}] Job submitted with ID: {self.job_id}")
             # Wait here for the monitoring to complete before exiting the process method