Fix workflow with name changes

myworkflow.cwl

@@ -8,11 +8,7 @@ inputs:
   - id: msin
     type: Directory
     'sbg:x': -379
-    'sbg:y': -136
-  - id: secondary_files
-    type: 'File[]'
-    'sbg:x': -903
-    'sbg:y': -511
+    'sbg:y': -172.47381591796875
   - id: strategy
     type: File?
     'sbg:x': -555.515625
@@ -22,7 +18,7 @@ outputs:
     outputSource:
       - dppp/msout
     type: Directory
-    'sbg:x': 70
+    'sbg:x': 108.00761413574219
     'sbg:y': -379
 steps:
   - id: dppp
@@ -33,45 +29,47 @@ steps:
         source: msin
       - id: secondary_files
         source:
-          - aoflagger_step_generator/secondary_files
+          - aoflagger_step_generator/output_secondary_files
     out:
       - id: msout
     run: steps/DPPPStep.cwl
-    'sbg:x': -125
-    'sbg:y': -414
+    'sbg:x': -77.87055969238281
+    'sbg:y': -458.0888366699219
   - id: average_step_generator
     in:
       - id: input_parset
-        source: _init_parset_generator/output_parset
-      - id: secondary_files
+        source: empty_parset_generator/output_parset
+      - id: input_secondary_files
         source:
-          - secondary_files
+          - empty_parset_generator/output_secondary_files
     out:
       - id: output_parset
-      - id: secondary_files
+      - id: output_secondary_files
     run: steps/AveragingStepGenerator.cwl
-    'sbg:x': -611.858642578125
-    'sbg:y': -452.00421142578125
-  - id: _init_parset_generator
-    in: []
-    out:
-      - id: output_parset
-    run: steps/InitParsetGenerator.cwl
-    'sbg:x': -914
-    'sbg:y': -354
+    'sbg:x': -659.6497192382812
+    'sbg:y': -479.365478515625
   - id: aoflagger_step_generator
     in:
       - id: input_parset
         source: average_step_generator/output_parset
-      - id: secondary_files
+      - id: input_secondary_files
         source:
-          - average_step_generator/secondary_files
+          - average_step_generator/output_secondary_files
       - id: strategy
         source: strategy
     out:
       - id: output_parset
-      - id: secondary_files
+      - id: output_secondary_files
     run: steps/AOFlaggerStepGenerator.cwl
-    'sbg:x': -398
-    'sbg:y': -451
-requirements: []
+    'sbg:x': -393.4390869140625
+    'sbg:y': -485.9670104980469
+  - id: empty_parset_generator
+    in: []
+    out:
+      - id: output_parset
+      - id: output_secondary_files
+    run: steps/EmptyParsetGenerator.cwl
+    'sbg:x': -903.7893676757812
+    'sbg:y': -480.0863037109375
+requirements:
+  - class: MultipleInputFeatureRequirement