fix toil bug #30

steps/LoSoTo.Faraday.cwl

@@ -6,6 +6,8 @@ id: losoto_faraday
 
 $namespaces:
   lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+$schema:
+  - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
 doc: |
   Faraday rotation extraction from either a rotation table or a
   circular phase (of which the operation get the polarisation difference).
@@ -69,5 +71,3 @@ outputs:
 
 stdout: $(inputs.input_h5parm.basename)-losoto.log
 stderr: $(inputs.input_h5parm.basename)-losoto_err.log
-$schema:
-  - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl

steps/LoSoTo.Polalign.cwl

@@ -14,32 +14,16 @@ doc: |
 requirements:
   InlineJavascriptRequirement:
     expressionLib:
-     - |
-        function get_config() {
-        var par = ['soltab = ' + inputs.soltab]
-        if (inputs.ncpu !== null) par.push('ncpu='+inputs.ncpu);
-        par.push('[polalign]')
-        par.push('operation = POLALIGN')
-        for(var field_name in inputs){
-            if(field_name === 'input_h5parm' ||
-               field_name === 'soltab' ||
-               field_name === 'ncpu') continue;
-            if(inputs[field_name] === null ||
-               inputs[field_name] === 'null') continue;
-            par.push(field_name+'='+inputs[field_name])
-        }
-        return par
-        }
+      - { $include: utils.js}
   InitialWorkDirRequirement:
     listing:
       - entryname: 'parset.config'
-        entry: $(get_config().join('\n'))
+        entry: $(get_losoto_config('POLALIGN').join('\n'))
+
       - entryname: $(inputs.input_h5parm.basename)
         entry: $(inputs.input_h5parm)
         writable: true
 
-
-
 baseCommand: "losoto"
 
 arguments:

workflows/linc_calibrator/fr.cwl

@@ -63,10 +63,11 @@ steps:
   - id: faraday_rot
     in:
       - id: refAnt
-        default: CS001HBA0
         source: refant
       - id: input_h5parm
         source: h5parm
+      - id: soltabout
+        default: faraday
     out:
       - id: output_h5parm
       - id: logfiles