Merge branch 'sensible-names-for-inline-scripts' into 'master'

Give inline scripts sensible names

See merge request eosc/prefactor3-cwl!55

Former-commit-id: f867357c [formerly 4ce78cad]
Former-commit-id: 9fbe6c96
Former-commit-id: 7950f383

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
\ No newline at end of file
+stderr: ms_concat_err.log

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)
\ No newline at end of file
+              json.dump({'msin': rendered_leafs}, fp, indent=4)

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
\ No newline at end of file
+stderr: findRefAnt_err.log