Give inline scripts sensible names

Some of the inline scripts (bash or python) have names like "script.py",
which is not very helpful for debugging. Renamed the scripts for those
workflows that contained either script.py or script.sh.

lofar-cwl/steps/ms_concat.cwl

@@ -5,7 +5,7 @@ $namespaces:
 id: ms_concat
 baseCommand:
   - /bin/bash
-  - script.sh
+  - ms_concat.sh
 inputs:
   - default: 50
     id: min_length
@@ -59,7 +59,7 @@ requirements:
     listing:
       - entry: $(inputs.msin)
         writable: true
-      - entryname: script.sh
+      - entryname: ms_concat.sh
         entry: |
           #!/bin/bash
           directories=\$(ls -d out_*)
@@ -71,4 +71,4 @@ requirements:
     inplaceUpdate: true
   - class: InlineJavascriptRequirement
 stdout: ms_concat.log
-stderr: ms_concat_err.log
+stderr: ms_concat_err.log
\ No newline at end of file

steps/aoflag.cwl

@@ -11,7 +11,7 @@ hints:
 baseCommand:
 #  - aoflagger
   - /bin/bash
-  - script.sh
+  - aoflag.sh
 inputs:
   - id: msin
     type: Directory[]
@@ -132,7 +132,7 @@ requirements:
         writable: true
       - entry: $(inputs.concat_additional_ms)
         writable: true
-      - entryname: script.sh
+      - entryname: aoflag.sh
         entry: |
           #!/bin/bash
           directories=\$(ls -d out*)

steps/compare_station_list.cwl

@@ -5,7 +5,7 @@ $namespaces:
 id: compare_station_list
 baseCommand:
   - python3
-  - script.py
+  - compare_station_list.py
 inputs:
     - id: msin
       type: Directory[]
@@ -27,7 +27,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: InitialWorkDirRequirement
     listing:
-      - entryname: script.py
+      - entryname: compare_station_list.py
         entry: |
           import sys
           import json

steps/create_workflow_input.cwl

@@ -18,12 +18,12 @@ outputs:
       
 baseCommand: 
   - python3
-  - script.py
+  - create_workflow_input.py
 doc: ''
 requirements:
   InitialWorkDirRequirement:
     listing:
-      - entryname: script.py
+      - entryname: create_workflow_input.py
         entry: | 
           #!/usr/bin/env python3
           
@@ -39,4 +39,4 @@ requirements:
               rendered_leafs.append(rendered_leaf)  
             
           with open('workflow_input.json', 'w') as fp:
-              json.dump({'msin': rendered_leafs}, fp, indent=4)
+              json.dump({'msin': rendered_leafs}, fp, indent=4)
\ No newline at end of file

steps/filter_ms_group.cwl

@@ -5,7 +5,7 @@ baseCommand:
   - python3
 arguments:
     - position: 0
-      valueFrom: script.py
+      valueFrom: filter_ms_group.py
 inputs:
   - id: group_id
     type: string
@@ -36,7 +36,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: InitialWorkDirRequirement
     listing:
-     - entryname: script.py
+     - entryname: filter_ms_group.py
        entry: |
         import sys
         import json

steps/findRefAnt_join.cwl

@@ -5,7 +5,7 @@ $namespaces:
 id: findRefAnt_join
 baseCommand:
   - python3
-  - script.py
+  - findRefAnt_join.py
 inputs:
     - id: flagged_fraction_dict
       type: string[]?
@@ -44,7 +44,7 @@ requirements:
     listing:
       - entryname: input.json
         entry: $(inputs.flagged_fraction_dict)
-      - entryname: script.py
+      - entryname: findRefAnt_join.py
         entry: |
             import sys
             import json
@@ -105,4 +105,4 @@ requirements:
                 json.dump(flagged_fraction_antenna, fp)
 
 stdout: findRefAnt.log
-stderr: findRefAnt_err.log
+stderr: findRefAnt_err.log
\ No newline at end of file