Quote library kit method in run.bash

StamLab · Jun 27, 2021 · 95be484 · 95be484
1 parent c6ff069
commit 95be484
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scripts/alignprocess.py b/scripts/alignprocess.py
@@ -342,7 +342,7 @@ def create_script(self, processing_info, align_id):
         env_vars["GENOME"]      = alignment['genome_index']
         env_vars["ASSAY"]       = lane['assay']
         env_vars["READLENGTH"]  = processing_info['flowcell']['read_length']
-        env_vars["LIBRARY_KIT"] = processing_info['libraries'][0]['library_kit_method']
+        env_vars["LIBRARY_KIT"] = '"' + processing_info['libraries'][0]['library_kit_method'] + '"'
 
         if processing_info['flowcell']['paired_end']:
             env_vars["PAIRED"] = "True"