Merge branch 'master' of git.astron.nl:eosc/lofar-cwl

Former-commit-id: 4e63512c

README.md

 # LOFAR-CWL
 
-Repository of LOFAR standard CWL steps
\ No newline at end of file
+Repository of LOFAR standard CWL steps.
+
+<img src="https://www.egi.eu/wp-content/uploads/2020/01/eu-logo.jpeg" alt="EU Flag" width="80">
+<img src="https://www.egi.eu/wp-content/uploads/2020/01/eosc-hub-v-web.png" alt="EOSC-hub logo" height="60">
+This work is co-funded by the EOSC-hub project (Horizon 2020) under Grant number 777536.

steps/DP3.Execute.cwl

@@ -6,7 +6,7 @@ $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 inputs:
   - id: msout_name
-    type: string
+    type: string?
     'sbg:x': -418
     'sbg:y': 187
   - id: msin

steps/DPPP.cwl

@@ -17,7 +17,7 @@ inputs:
       prefix: msin=
       separate: false
     doc: Input Measurement Set
-  - default: out.MS
+  - default: "."
     id: msout_name
     type: string
     inputBinding:
@@ -37,46 +37,46 @@ inputs:
   - id: output_directory_names
     type: Any
     doc: Expected output file names
-  - default: true
+  - default: false
     id: autoweight
     type: boolean
     inputBinding:
       position: 0
-      prefix: '-msin.autoweight=True'
+      prefix: 'msin.autoweight=True'
   - default: "dysco"
     id: storagemanager
     type: string
     inputBinding:
       position: 0
-      prefix: '-msout.storagemanager='
+      prefix: 'msout.storagemanager='
       separate: false
   - default: ''
     id: baseline
     type: string
     inputBinding:
       position: 0
-      prefix: '-msin.baseline='
+      prefix: 'msin.baseline='
       separate: false
   - default: DATA
     id: output_column
     type: string?
     inputBinding:
       position: 0
-      prefix: '-msout.datacolumn='
+      prefix: 'msout.datacolumn='
       separate: false
   - default: DATA
     id: input_column
     type: string?
     inputBinding:
       position: 0
-      prefix: '-msin.datacolumn='
+      prefix: 'msin.datacolumn='
       separate: false
 outputs:
   - id: msout
     doc: Output Measurement Set
     type: Directory
     outputBinding:
-      glob: '$(inputs.msout_name=="."?inputs.msin:inputs.msout_name)'
+      glob: '$(inputs.msout_name=="." ? inputs.msin.basename : inputs.msout_name)'
   - id: secondary_output_files
     doc: Secondary output files
     type: Any
@@ -121,3 +121,7 @@ hints:
 stdout: DPPP.log
 requirements:
   - class: InlineJavascriptRequirement
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.msin)
+        writable: true

steps/LoSoTo.Residual.cwl

@@ -49,7 +49,7 @@ inputs:
 outputs:
   - id: output_h5parm
     type: File
-    format: lofar#H5Parm
+    format: lofar:#H5Parm
     outputBinding:
       glob: $(inputs.input_h5parm.basename)
 

steps/applycal.cwl

@@ -51,7 +51,7 @@ inputs:
   - id: storagemanager
     type: string
     default: dysco
-    inputBinding
+    inputBinding:
       prefix: msout.storagemanager=
   - id: updateweights
     type: boolean?

steps/ddecal.cwl

@@ -7,6 +7,10 @@ baseCommand: [DPPP]
 
 requirements:
   InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entry: $(inputs.msin)
+        writable: true
 
 hints:
   DockerRequirement:
@@ -26,7 +30,7 @@ arguments:
 
 inputs:
   - id: msin
-    type: Directory?
+    type: Directory
     doc: Input Measurement Set
     inputBinding:
       prefix: msin=
@@ -57,7 +61,7 @@ inputs:
   - id: msout_name
     type: string
     doc: Output Measurement Set
-    default: out.MS
+    default: "OUT.MS"
     inputBinding:
       prefix: msout=
       separate: false
@@ -93,8 +97,9 @@ inputs:
   - id: storagemanager
     type: string
     default: dysco
-    inputBinding
+    inputBinding:
       prefix: msout.storagemanager=
+      separate: false
   - id: mode
     type:
       type: enum
@@ -120,12 +125,12 @@ outputs:
     doc: Output Measurement Set
     type: Directory
     outputBinding:
-      glob: $(inputs.msout_name=="."?inputs.msin:inputs.msout_name)
+      glob: $(inputs.msin.basename)
 
   - id: h5parm
     doc: Filename of output H5Parm (to be read by e.g. losoto)
     type: File
-    format: lofar:#H5Parm
+    format: 'lofar:#H5Parm'
     outputBinding:
       glob: $(inputs.output_name_h5parm)
 

steps/predict.cwl

@@ -24,8 +24,8 @@ inputs:
   - id: storagemanager
     type: string
     default: dysco
-    inputBinding
-      prefix: msout.storagemanager=  
+    inputBinding:
+      prefix: msout.storagemanager=
   - default: MODEL_DATA
     id: msout_datacolumn
     type: string