strip output_dir when normalizing mags record

nmdc_automation/models/nmdc.py

@@ -81,6 +81,9 @@ def _normalize_mags_record(record: Dict[str, Any]) -> Dict[str, Any]:
         # for backwards compatibility normalize num_tRNA to num_t_rna
         if "num_tRNA" in mag:
             record["mags_list"][i]["num_t_rna"] = mag.pop("num_tRNA")
+        # strip output_dir if present
+        if "output_dir" in mag:
+            record["mags_list"][i].pop("output_dir")
         # add type to eukaryotic_evaluation if it exists
         if "eukaryotic_evaluation" in mag:
             record["mags_list"][i]["eukaryotic_evaluation"]["type"] = "nmdc:EukEval"

nmdc_automation/workflow_automation/wfutils.py

@@ -512,7 +512,7 @@ def make_data_objects(self, output_dir: Union[str, Path] = None) -> List[DataObj
 
     def make_workflow_execution(self, data_objects: List[DataObject]) -> WorkflowExecution:
         """
-        Create a workflow execution record for the job. This record includes the basic workflow execution attributes
+        Create a workflow execution instance for the job. This record includes the basic workflow execution attributes
         and the data objects generated by the job. Additional workflow-specific attributes can be defined in the
         workflow execution template and read from a job's output files.
         The data objects are added to the record as a list of IDs in the "has_output" key.