add stderr and Dysco

lofar-cwl/steps/applybeam.cwl

@@ -41,9 +41,14 @@ inputs:
       except for full Jones, in which case correction should be 'fulljones'.
   - id: storagemanager
     type: string
-    default: dysco
+    default: ""
     inputBinding:
       prefix: msout.storagemanager=
+  - id: databitrate
+    type: int?
+    inputBinding:
+       prefix: msout.storagemanager.databitrate=
+       separate: false
   - id: updateweights
     type: string?
     inputBinding:
@@ -76,10 +81,11 @@ outputs:
     outputBinding:
       glob: $(inputs.msin.basename)
   - id: logfile
-    type: File
+    type: File[]
     outputBinding:
-      glob: applycal_$(inputs.type).log    
+      glob: 'applycal_$(inputs.type)*.log'
 stdout: applycal_$(inputs.type).log
+stderr: applycal_$(inputs.type)_err.log
 arguments:
   - 'steps=[applybeam]'
   - msout=.

lofar-cwl/steps/applycal.cwl

@@ -50,9 +50,14 @@ inputs:
       except for full Jones, in which case correction should be 'fulljones'.
   - id: storagemanager
     type: string
-    default: dysco
+    default: ""
     inputBinding:
       prefix: msout.storagemanager=
+  - id: databitrate
+    type: int?
+    inputBinding:
+       prefix: msout.storagemanager.databitrate=
+       separate: false
   - id: updateweights
     type: string?
     inputBinding:
@@ -66,10 +71,11 @@ outputs:
     outputBinding:
       glob: $(inputs.msin.basename)
   - id: logfile
-    type: File
+    type: File[]
     outputBinding:
-      glob: applycal_$(inputs.correction).log   
+      glob: 'applycal_$(inputs.correction)*.log'
 stdout: applycal_$(inputs.correction).log
+stderr: applycal_$(inputs.correction)_err.log
 arguments:
   - 'steps=[applycal]'
   - msout=.

lofar-cwl/steps/predict.cwl

@@ -61,13 +61,12 @@ inputs:
        prefix: msout.overwrite=True
   - id: storagemanager
     type: string
-    default: "Dysco"
+    default: ""
     inputBinding:
        prefix: msout.storagemanager=
        separate: false
   - id: databitrate
-    type: int
-    default: 0
+    type: int?
     inputBinding:
        prefix: msout.storagemanager.databitrate=
        separate: false

subworkflow/apply_calibrate_bp.cwl

@@ -28,7 +28,7 @@ inputs:
 outputs:
   - id: apply_fr.log
     outputSource:
-      - applyFR/logfile
+      - concat_logfiles_applyFR/output
     type: File
     'sbg:x': 1000
     'sbg:y': -300
@@ -46,7 +46,7 @@ outputs:
     'sbg:y': -100
   - id: apply_cal.log
     outputSource:
-      - applyBP/logfile
+      - concat_logfiles_applyBP/output
     type: File
     'sbg:x': 1000
     'sbg:y': 0
@@ -64,7 +64,7 @@ outputs:
     'sbg:y': 200
   - id: apply_pa.log
     outputSource:
-      - applyPA/logfile
+      - concat_logfiles_applyPA/output
     type: File
     'sbg:x': 1000
     'sbg:y': 300
@@ -79,6 +79,10 @@ steps:
         source: input_h5parm
       - id: msout_datacolumn
         default: CORRECTED_DATA
+      - id: storagemanager
+        default: Dysco
+      - id: databitrate
+        default: 0
       - id: correction
         default: polalign
     out:
@@ -94,14 +98,18 @@ steps:
         source: applyPA/msout
       - id: msin_datacolumn
         default: CORRECTED_DATA
-      - id: updateweights
-        default: 'True'
       - id: parmdb
         source: input_h5parm
       - id: msout_datacolumn
         default: CORRECTED_DATA
+      - id: storagemanager
+        default: Dysco
+      - id: databitrate
+        default: 0
       - id: correction
         default: bandpass
+      - id: updateweights
+        default: 'True'
     out:
       - id: msout
       - id: logfile
@@ -111,22 +119,26 @@ steps:
     'sbg:y': 0
   - id: applybeam
     in:
+      - id: msin
+        source: applyBP/msout
       - id: msin_datacolumn
         default: CORRECTED_DATA
       - id: msout_datacolumn
         default: CORRECTED_DATA
+      - id: storagemanager
+        default: Dysco
+      - id: databitrate
+        default: 0
+      - id: type
+        default: applybeam
       - id: updateweights
         default: 'true'
+      - id: usechannelfreq
+        default: 'false'
       - id: invert
         default: 'true'
       - id: beammode
         default: element
-      - id: usechannelfreq
-        default: 'false'
-      - id: msin
-        source: applyBP/msout
-      - id: type
-        default: applybeam
     out:
       - id: msout
       - id: logfile
@@ -144,6 +156,10 @@ steps:
         source: input_h5parm
       - id: msout_datacolumn
         default: CORRECTED_DATA
+      - id: storagemanager
+        default: Dysco
+      - id: databitrate
+        default: 0
       - id: correction
         default: faraday
     out:
@@ -176,10 +192,10 @@ steps:
         default: SMOOTHED_DATA
       - id: msin_modelcolum
         default: MODEL_DATA
-      - id: flagunconverged
-        source: flagunconverged
       - id: propagate_solutions
         source: propagatesolutions
+      - id: flagunconverged
+        source: flagunconverged
       - id: mode
         default: diagonal
     out:
@@ -202,4 +218,56 @@ steps:
     label: concat_logfiles_calib_cal
     'sbg:x': 700
     'sbg:y': 200
+  - id: concat_logfiles_applyFR
+    in:
+      - id: file_list
+        source:
+          - applyFR/logfile
+      - id: file_prefix
+        default: applycal
+    out:
+      - id: output
+    run: ../steps/concatenate_files.cwl
+    label: concat_logfiles_applyFR
+    'sbg:x': 400
+    'sbg:y': 200
+  - id: concat_logfiles_applybeam
+    in:
+      - id: file_list
+        source:
+          - applybeam/logfile
+      - id: file_prefix
+        default: applybeam
+    out:
+      - id: output
+    run: ../steps/concatenate_files.cwl
+    label: concat_logfiles_applybeam
+    'sbg:x': 200
+    'sbg:y': 200
+  - id: concat_logfiles_applyBP
+    in:
+      - id: file_list
+        source:
+          - applyBP/logfile
+      - id: file_prefix
+        default: applycal
+    out:
+      - id: output
+    run: ../steps/concatenate_files.cwl
+    label: concat_logfiles_applBP
+    'sbg:x': 0
+    'sbg:y': 200
+  - id: concat_logfiles_applyPA
+    in:
+      - id: file_list
+        source:
+          - applyPA/logfile
+      - id: file_prefix
+        default: applycal
+    out:
+      - id: output
+    run: ../steps/concatenate_files.cwl
+    label: concat_logfiles_applyPA
+    'sbg:x': -200
+    'sbg:y': 200
 requirements: []

subworkflow/apply_calibrate_fr.cwl

@@ -40,7 +40,7 @@ outputs:
     'sbg:y': -100
   - id: apply_cal.log
     outputSource:
-      - applyFR/logfile
+      - concat_logfiles_applycal/output
     type: File
     'sbg:x': 1000
     'sbg:y': 0
@@ -67,6 +67,10 @@ steps:
         source: input_h5parm
       - id: msout_datacolumn
         default: CORRECTED_DATA
+      - id: storagemanager
+        default: Dysco
+      - id: databitrate
+        default: 0
       - id: correction
         default: faraday
     out:
@@ -125,4 +129,17 @@ steps:
     label: concat_logfiles_calib_cal
     'sbg:x': 700
     'sbg:y': 200
+  - id: concat_logfiles_applycal
+    in:
+      - id: file_list
+        source:
+          - applyFR/logfile
+      - id: file_prefix
+        default: applycal
+    out:
+      - id: output
+    run: ../steps/concatenate_files.cwl
+    label: concat_logfiles_applycal
+    'sbg:x': -200
+    'sbg:y': 200
 requirements: []

subworkflow/apply_calibrate_pa.cwl

@@ -40,7 +40,7 @@ outputs:
     'sbg:y': -100
   - id: apply_cal.log
     outputSource:
-      - applyPA/logfile
+      - concat_logfiles_applycal/output
     type: File
     'sbg:x': 1000
     'sbg:y': 0
@@ -58,7 +58,7 @@ outputs:
     'sbg:y': 200
   - id: applybeam.log
     outputSource:
-      - applybeam/logfile
+      - concat_logfiles_applybeam/output
     type: File
     'sbg:x': 1000
     'sbg:y': 300
@@ -73,6 +73,10 @@ steps:
         source: input_h5parm
       - id: msout_datacolumn
         default: CORRECTED_DATA
+      - id: storagemanager
+        default: Dysco
+      - id: databitrate
+        default: 0
       - id: correction
         default: polalign
     out:
@@ -88,6 +92,10 @@ steps:
         default: CORRECTED_DATA
       - id: msout_datacolumn
         default: CORRECTED_DATA
+      - id: storagemanager
+        default: Dysco
+      - id: databitrate
+        default: 0
       - id: updateweights
         default: 'true'
       - id: invert
@@ -156,4 +164,30 @@ steps:
     label: concat_logfiles_calib_cal
     'sbg:x': 700
     'sbg:y': 200
+  - id: concat_logfiles_applybeam
+    in:
+      - id: file_list
+        source:
+          - applybeam/logfile
+      - id: file_prefix
+        default: applybeam
+    out:
+      - id: output
+    run: ../steps/concatenate_files.cwl
+    label: concat_logfiles_applybeam
+    'sbg:x': 0
+    'sbg:y': 200
+  - id: concat_logfiles_applycal
+    in:
+      - id: file_list
+        source:
+          - applyPA/logfile
+      - id: file_prefix
+        default: applycal
+    out:
+      - id: output
+    run: ../steps/concatenate_files.cwl
+    label: concat_logfiles_applycal
+    'sbg:x': -200
+    'sbg:y': 200
 requirements: []