Rename parameters_input to steps

Former-commit-id: 42354972

steps/DP3.AOFlaggerStepGenerator.cwl

@@ -5,7 +5,7 @@ cwlVersion: v1.0
 id: aoflagger_step_generator
 
 inputs:
-  - id: parameters_input
+  - id: steps
     type: Any[]?
     default: []
   - id: step_name
@@ -95,8 +95,8 @@ steps:
         default: 'aoflagger'
       - id: step_id
         source: step_name
-      - id: parameters_input
-        source: parameters_input
+      - id: steps
+        source: steps
       - id: parameters
         valueFrom: $(inputs)
       - id: count.save

steps/DP3.AveragerStepGenerator.cwl

@@ -60,7 +60,7 @@ steps:
         default: 'averager'
       - id: step_id
         source: step_name
-      - id: parameters_input
+      - id: steps
         source: input_parset
       - id: parameters
         valueFrom: $(inputs)

steps/DP3.DemixerStepGenerator.cwl

@@ -7,7 +7,7 @@ $namespaces:
 id: demix_step_generator
 
 inputs:
-  - id: parameters_input
+  - id: steps
     type: Any[]?
     default: []
   - id: step_name
@@ -134,8 +134,8 @@ outputs:
 steps:
   - id: DP3_GenericStep
     in:
-    - id: parameters_input
-      source: parameters_input
+    - id: steps
+      source: steps
     - id: output_files
       default: ["instrumentmodel"]
       

steps/DP3.GenericStep.cwl

@@ -8,7 +8,7 @@ requirements:
   - class: InlineJavascriptRequirement
 
 inputs:
-  - id: parameters_input
+  - id: steps
     type: Any[]
 
   - id: parameters
@@ -36,9 +36,9 @@ expression: |-
 
    delete inputs.parameters.step_type;
    delete inputs.parameters.step_id;
-   delete inputs.parameters.parameters_input;
+   delete inputs.parameters.steps;
    delete inputs.parameters.parameters;
-   delete inputs.parameters.parameters_input;
+   delete inputs.parameters.steps;
 
 
    var new_step = {'step_type': step_type,
@@ -47,7 +47,7 @@ expression: |-
                    'output_files': output_files};
 
 
-   var in_parameters = inputs.parameters_input;
+   var in_parameters = inputs.steps;
 
    // Checks if the step_id is duplicate if so raised an exception
    var step_ids = []

steps/DP3.ParsetGenerator.cwl

@@ -18,7 +18,7 @@ arguments:
         true = True
         false = False
         null = None
-        steps_list = $(inputs.parameters_input)
+        steps_list = $(inputs.steps)
         steps_id_list = list(map(lambda item: item['step_id'], steps_list))
 
         for step in steps_list:
@@ -50,7 +50,7 @@ arguments:
         last_step_line = 'steps=[%s]' % ', '.join(steps_id_list)
         print(last_step_line)
 inputs:
-  - id: parameters_input
+  - id: steps
     type: Any[]?
 
 outputs:
@@ -66,8 +66,8 @@ outputs:
       outputEval: |-
         ${
         var outfiles = []
-        for(var step in inputs.parameters_input){
-          step = inputs.parameters_input[step]
+        for(var step in inputs.steps){
+          step = inputs.steps[step]
           for(var parameter in step['parameters']){
             parameter = step['parameters'][parameter]
 
@@ -85,8 +85,8 @@ outputs:
       outputEval: |
         ${
         var outdirs = []
-        for(var step in inputs.parameters_input){
-          step = inputs.parameters_input[step]
+        for(var step in inputs.steps){
+          step = inputs.steps[step]
           for(var parameter in step['parameters']){
             parameter = step['parameters'][parameter]
             if (parameter != null && parameter.class=='Directory'){
@@ -104,8 +104,8 @@ outputs:
       outputEval: |
         ${
         var out_names = {}
-        for(var step_idx in inputs.parameters_input){
-          var step = inputs.parameters_input[step_idx]
+        for(var step_idx in inputs.steps){
+          var step = inputs.steps[step_idx]
           var step_id = step['step_id']
           var step_dirs = {}
           if(!step.hasOwnProperty("output_files")) continue;
@@ -129,8 +129,8 @@ outputs:
       outputEval: |-
         ${
         var out_names = {}
-        for(var step_idx in inputs.parameters_input){
-          var step = inputs.parameters_input[step_idx]
+        for(var step_idx in inputs.steps){
+          var step = inputs.steps[step_idx]
           var step_id = step['step_id']
           var step_dirs = {}
           if(!step.hasOwnProperty("output_directories")) continue;

steps/DP3.PreflaggerStepGenerator.cwl

@@ -181,7 +181,7 @@ steps:
         default: 'preflagger'
       - id: step_id
         source: step_name
-      - id: parameters_input
+      - id: steps
         source: input_parset
       - id: parameters
         valueFrom: $(inputs)

subworkflow/ndppp_prep_cal.cwl

@@ -116,7 +116,7 @@ steps:
     'sbg:y': -119.96077728271484
   - id: aoflag
     in:
-      - id: parameters_input
+      - id: steps
         source:
           - flagedge/parameters_out
       - id: step_name
@@ -148,7 +148,7 @@ steps:
     'sbg:y': -44.651588439941406
   - id: demixstepgenerator
     in:
-      - id: parameters_input
+      - id: steps
         source:
           - flagamp/parameters_out
     out:
@@ -158,7 +158,7 @@ steps:
     'sbg:y': 156.3474578857422
   - id: parsetgenerator
     in:
-      - id: parameters_input
+      - id: steps
         source:
           - demix_select/output_arguments
     out:

test_workflow/flag_average.cwl

@@ -36,7 +36,7 @@ steps:
     'sbg:y': -729
   - id: parset_generator
     in:
-      - id: parameters_input
+      - id: steps
         source:
           - average_step_generator/parameters_out
     out: