only record create_job on top level workflow

Author: stain

cwltool/workflow.py

@@ -566,8 +566,11 @@ def job(self,
         builder = self._init_job(job_order, runtimeContext)
         #relativeJob=copy.deepcopy(builder.job)
         if runtimeContext.research_obj:
-            runtimeContext.research_obj.make_fs_access = runtimeContext.make_fs_access
-            runtimeContext.research_obj.create_job(self.job, builder.job)
+            if not runtimeContext.research_obj.make_fs_access:
+                runtimeContext.research_obj.make_fs_access = runtimeContext.make_fs_access
+            if runtimeContext.toplevel:
+                # Record primary-job.json
+                runtimeContext.research_obj.create_job(self.job, builder.job)
 
         job = WorkflowJob(self, runtimeContext)
         yield job