Set default to false for file removal in file upload

VERSIONLOG.md

@@ -1,5 +1,9 @@
 # Scilifelab_epps Version Log
 
+## 20251113.1
+
+Set default to false for file removal in file upload, pass parameter as false in aviti samplesheet generation just to be on the safe side
+
 ## 20251105.1
 
 Fix bugs in ONT couchdb connections

scilifelab_epps/epp.py

@@ -558,7 +558,7 @@ def upload_file(
     file_slot: str,
     process: Process,
     lims: Lims,
-    remove: bool = True,
+    remove: bool = False,
     fail_on_missing_file_slot: bool = True,
 ):
     matching_file_slots = [

scripts/generate_aviti_run_manifest.py

@@ -583,6 +583,7 @@ def main(args: Namespace):
         args.file,
         process,
         lims,
+        remove=False,
     )
 
     # Move manifest(s)