--leave-tmpdir includes the input staging directories (#1674)

Author: mr-c

cwltool/job.py

@@ -439,7 +439,7 @@ def stderr_stdout_log_path(
             with runtimeContext.workflow_eval_lock:
                 self.output_callback(outputs, processStatus)
 
-        if self.stagedir is not None and os.path.exists(self.stagedir):
+        if runtimeContext.rm_tmpdir and self.stagedir is not None and os.path.exists(self.stagedir):
             _logger.debug(
                 "[job %s] Removing input staging directory %s",
                 self.name,