Fixes to run_batches

run_batches.py

@@ -39,6 +39,8 @@ def main():
         input_files_batch = list(input_files)[: args.batch_size]
 
         with TemporaryDirectory() as temp_dir_SR, TemporaryDirectory() as temp_dir_GNR, TemporaryDirectory() as temp_dir_SA, TemporaryDirectory() as input_temp_dir, TemporaryDirectory() as output_temp_dir:
+            input_temp_dir = Path(input_temp_dir)
+            output_temp_dir = Path(output_temp_dir)
             for file in input_files_batch:
                 shutil.copy(input_dir / file, input_temp_dir)
 
@@ -60,11 +62,11 @@ def main():
                     logging.exception(f"Error running command: {command}")
                     raise e
 
-            output_files = output_temp_dir.rglob("*")
+            output_paths = output_temp_dir.rglob("*")
             output_files = set(file.name for file in output_files)
-            for file in output_files:
-                shutil.copy(file, output_dir)
-                input_files.remove(file)
+            for output_path, output_file in zip(output_paths, output_files):
+                shutil.copy(output_path, output_dir)
+                input_files.remove(output_file)
             end = time.time()
             logging.info(f"Processed {len(output_files)} files in {timedelta(seconds=end - start)}")