From ebdc0c314e911b06d56ac79f17c9de6b27429f06 Mon Sep 17 00:00:00 2001
From: Eric Charles <badass@stanford.edu>
Date: Wed, 3 Apr 2024 11:10:17 -0700
Subject: [PATCH] fix file closing not to overwrite files when running in
 chunked mode (#100)

---
 src/rail/core/stage.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/rail/core/stage.py b/src/rail/core/stage.py
index 7570e6ed..9e288a8a 100644
--- a/src/rail/core/stage.py
+++ b/src/rail/core/stage.py
@@ -396,7 +396,8 @@ def _finalize_tag(self, tag):
         """
         handle = self.get_handle(tag, allow_missing=True)
         if self.config.output_mode == 'default':
-            handle.write()
+            if not os.path.exists(handle.path) or not handle.partial:
+                handle.write()            
         final_name = PipelineStage._finalize_tag(self, tag)
         handle.path = final_name
         return final_name