Update pipeline.py

pipeline.py

@@ -433,7 +433,7 @@ def pipeline_with_gemini(accessions,stop_flag=None, niche_cases=None):
         # else: 
         #   print("no suceed, fallback to all tem links")
         #   links = tem_links
-        links = smart_fallback.filter_links_by_metadata(tem_links, saveLinkFolder=sample_folder_id, accession=acc)
+        links = smart_fallback.filter_links_by_metadata(tem_links, saveLinkFolder=sample_folder_id, accession=acc, stop_flag=stop_flag)
       print("this is links: ",links)    
       links = unique_preserve_order(links)
       acc_score["source"] = links