Only delete working/ and outputs on resubmission

lib/galaxy/jobs/__init__.py

@@ -1113,6 +1113,7 @@ class JobWrapper(HasResourceParameters):
             # The tool execution is given a working directory beneath the
             # "job" working directory.
             safe_makedirs(self.tool_working_directory)
+            safe_makedirs(os.path.join(working_directory, 'outputs'))
             log.debug('(%s) Working directory for job is: %s',
                       self.job_id, self.working_directory)
         except ObjectInvalid:

lib/galaxy/jobs/command_factory.py

@@ -101,7 +101,13 @@ def build_command(
 
         # Remove the working directory incase this is for instance a SLURM re-submission.
         # xref https://github.com/galaxyproject/galaxy/issues/3289
-        commands_builder.prepend_command("rm -rf working outputs; mkdir -p working outputs; cd working")
+        commands_builder.prepend_command("""# Delete working/ and outputs/ only if job was resubmitted
+if [ -f .job_started ]; then
+    rm -rf working outputs; mkdir -p working outputs
+fi
+touch .job_started
+cd working
+""", sep='')
 
     container_monitor_command = job_wrapper.container_monitor_command(container)
     if container_monitor_command:

lib/galaxy/tools/__init__.py

@@ -2269,9 +2269,8 @@ class OutputParameterJSONTool(Tool):
             json_params['output_data'].append(data_dict)
             if json_filename is None:
                 json_filename = file_name
-        out = open(json_filename, 'w')
-        out.write(json.dumps(json_params))
-        out.close()
+        with open(json_filename, 'w') as out:
+            out.write(json.dumps(json_params))
 
 
 class ExpressionTool(Tool):