bugfixes

steps/check_unflagged_fraction.cwl

@@ -48,7 +48,7 @@ outputs:
   - id: msout
     type: Directory[]
     outputBinding:
-        glob: 'L*.ms.dpppconcat'
+        glob: 'L*.dpppconcat'
   - id: unflagged_fraction
     type: float
     outputBinding:

steps/identify_bad_antennas.cwl

@@ -21,7 +21,6 @@ arguments:
     from identifyBadAntennas_CWL import main as identifyBadAntennas
     
     ms = sys.argv[1]
-    filter = '$(inputs.filter)'
 
     output = identifyBadAntennas(ms)
 

steps/identify_bad_antennas_join.cwl

@@ -19,18 +19,21 @@ label: identifyBadAntennas_join
 arguments:
   - '-c'
   - |
-
-    flaggedants_list = sys.argv[1:]
+  
+    import sys
+    import json
+    
+    flaggedants = $(inputs.flaggedants)
     filter = '$(inputs.filter)'
+
     
+    flaggedants_list = [ flaggedant.split(',') for flaggedant in flaggedants ]
     flagged_antenna_list = set.intersection(*map(set, flaggedants_list)) 
-    
+
     for flagged_antenna in flagged_antenna_list:
         filter += ';!' + flagged_antenna + '*&&*'
 
-    print('Identified bad antennas: ' + str(flagged_antenna_list))
-    
-    cwl_output  = {"filter": str(filter)}
+    cwl_output  = {"filter": filter}
 
     with open('./out.json', 'w') as fp:
         json.dump(cwl_output, fp)