--leave-tmpdir includes the input staging directories

Author: mr-c

cwltool/job.py

@@ -460,7 +460,11 @@ 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,