Add index files to saved files

src/ng6/ng6workflow.py

@@ -686,7 +686,7 @@ class CasavaNG6Workflow(NG6Workflow):
 
             # archive the files
             #TODO : if self.group_prefix == None, the create the output of fastqilluminafilter in the run.get_work_directory()
-            saved_files = filtered_read1_files + filtered_read2_files
+            saved_files = filtered_read1_files + filtered_read2_files + self.get_all_reads("index")
             logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files))
             reads_prefixes = None
             if self.group_prefix != None :