more flu fixes

Author: dpark01

pipes/WDL/tasks/tasks_ncbi.wdl

@@ -887,9 +887,11 @@ task biosample_to_genbank {
               ### Influenza-specific isolate naming was handled above already and is required to be metadata-free
               # FTP submission pathway requires us to do the naming via the strain field
               type = outrow['organism'].split()[1] # A, B, C, D, etc
-              state = outrow['geo_loc_name'].split(':')[1] if ':' in outrow['geo_loc_name'] else outrow['geo_loc_name']
+              state = outrow['geo_loc_name'].split(':')[1].strip() if ':' in outrow['geo_loc_name'] else outrow['geo_loc_name']
               year = outrow['collection_date'].split('-')[0]
               outrow['strain'] = '/'.join([type, state, outrow['isolate'], year])
+              if type == 'A':
+                outrow['strain'] = '{}({})'.format(outrow['strain'], outrow['serotype'])
               print("new strain name: {}".format(outrow['strain']))
             elif outrow['organism'].startswith('Special taxon with special naming rules'):
               ### Example special case here