Refactor steps

steps/H5ParmCollector.cwl

-#!/usr/bin/env cwl-runner
-
 class: CommandLineTool
 cwlVersion: v1.0
+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
 id: h5parm_collector
-
-hints:
-  DockerRequirement:
-    dockerPull: lofareosc/prefactor-ci:master
-
 baseCommand:
   - H5parm_collector.py
 inputs:
   - id: h5parmFiles
-    type: File[]
-    doc: List of h5parm files
+    type: 'File[]'
     inputBinding:
       position: 0
-  - id: insolset
+    doc: List of h5parm files
+  - default: sol000
+    id: insolset
     type: string?
-    default: sol000
-    doc: Input solset name
     inputBinding:
-      prefix: --insolset
-  - id: outh5parmname
+      position: 0
+      prefix: '--insolset'
+    doc: Input solset name
+  - default: output.h5
+    id: outh5parmname
     type: string
     doc: Output h5parm name
-    default: output.h5
-
+  - id: squeeze
+    type: boolean
+    inputBinding:
+      position: 0
+      prefix: '-q'
+    doc: removes all axes with the length of 1
+  - default: true
+    id: verbose
+    type: boolean
+    inputBinding:
+      position: 0
+      prefix: '-v'
+    doc: verbose output
+  - default: true
+    id: clobber
+    type: boolean
+    inputBinding:
+      position: 0
+      prefix: '-c'
+    doc: overwrite output
 outputs:
   - id: outh5parm
     doc: Output h5parm
     type: File
     outputBinding:
       glob: $(inputs.outh5parmname)
+  - id: log
+    type: File
+    outputBinding:
+      glob: $(inputs.outh5parmname)-parm_collector_output.log
 label: H5parm_collector
+hints:
+  - class: DockerRequirement
+    dockerPull: 'lofareosc/prefactor-ci:master'
+stdout: $(inputs.outh5parmname)-parm_collector_output.log
+requirements:
+  - class: InlineJavascriptRequirement

steps/blsmooth.cwl

@@ -2,8 +2,6 @@ class: CommandLineTool
 cwlVersion: v1.0
 id: blsmooth
 label: BLsmooth
-arguments:
-  - '-S SMOOTH'
 baseCommand:
   - BLsmooth.py
 inputs:
@@ -19,6 +17,12 @@ inputs:
       position: 0
       prefix: '-f'
     doc: Gives an indication on how strong is the ionosphere
+  - id: do_smooth
+    type: boolean
+    doc: 'If true performs smoothing'
+    inputBinding: 
+      prefix: '--smooth=SMOOTH'
+      
   - default: 0.5
     id: bscalefactor
     type: float

steps/ddecal.cwl

@@ -23,6 +23,7 @@ arguments:
   - ddecal.flagdivergedonly=True
   - ddecal.tolerance=1.e-3
   - ddecal.usemodelcolumn=True
+  
 
 inputs:
   - id: msin
@@ -63,6 +64,11 @@ inputs:
         separate: false
         
 #--------------------
+  - id: propagate_solutions
+    type: boolean
+    default: true
+    inputBinding:
+      prefix: propagatesolutions=True
   - id: flagunconverged
     type: boolean
     default: false

subworkflow/calib_cal.cwl

@@ -7,30 +7,44 @@ $namespaces:
 inputs:
   - id: msin
     type: Directory
-    'sbg:x': -613.3988647460938
-    'sbg:y': 29.5
+    'sbg:x': -752
+    'sbg:y': -23
   - id: skymodels
     type: Directory
-    'sbg:x': -576.3988647460938
-    'sbg:y': -294.5
+    'sbg:x': -626
+    'sbg:y': -302
+  - id: flagunconverged
+    type: boolean
+    'sbg:x': 41
+    'sbg:y': 100
+  - id: propagate_solutions
+    type: boolean
+    'sbg:x': 77.1015625
+    'sbg:y': -259
+  - id: do_smooth
+    type: boolean
+    'sbg:x': -604
+    'sbg:y': 123
 outputs:
   - id: h5parm
     outputSource:
-      - ddecal/h5parm
+      - calib_cal/h5parm
     type: File
-    'sbg:x': 381.60113525390625
-    'sbg:y': -9.5
+    'sbg:x': 429
+    'sbg:y': -52
   - id: msout
     outputSource:
-      - ddecal/msout
+      - calib_cal/msout
     type: Directory
-    'sbg:x': 394.60113525390625
-    'sbg:y': -137.5
+    'sbg:x': 404
+    'sbg:y': -227
 steps:
   - id: blsmooth
     in:
       - id: msin
         source: msin
+      - id: do_smooth
+        source: do_smooth
     out:
       - id: msout
     run: ../steps/blsmooth.cwl
@@ -42,7 +56,7 @@ steps:
       - id: msin
         source: blsmooth/msout
       - id: sources_db
-        source: make_sourcedb_ateam/output
+        source: make_sourcedb/output
     out:
       - id: msout
     run: ../steps/predict.cwl
@@ -51,8 +65,7 @@ steps:
   - id: find_skymodel_cal_py
     in:
       - id: msin
-        source:
-          - msin
+        source: msin
       - id: skymodels
         source: skymodels
     out:
@@ -61,26 +74,30 @@ steps:
     label: find_skymodel_cal.py
     'sbg:x': -416
     'sbg:y': -209
-  - id: make_sourcedb_ateam
+  - id: make_sourcedb
     in:
       - id: sky_model
         source: find_skymodel_cal_py/output_models
     out:
       - id: output
     run: ../steps/makesourcedb.cwl
-    label: make_sourcedb_ateam
+    label: make_sourcedb
     'sbg:x': -221
     'sbg:y': -217
-  - id: ddecal
+  - id: calib_cal
     in:
       - id: msin
         source: predict/msout
       - id: msin_datacolumn
         default: SMOOTHED_DATA
+      - id: propagate_solutions
+        source: propagate_solutions
+      - id: flagunconverged
+        source: flagunconverged
     out:
       - id: msout
       - id: h5parm
     run: ../steps/ddecal.cwl
     'sbg:x': 222
     'sbg:y': -89
-requirements: []
\ No newline at end of file
+requirements: []

workflows/prefactor_calibrator.cwl

@@ -7,20 +7,52 @@ $namespaces:
 inputs:
   - id: raw_data
     type: boolean
-    'sbg:x': -620
-    'sbg:y': -683
+    'sbg:x': -798
+    'sbg:y': -680
   - id: demix
     type: boolean
-    'sbg:x': -617
-    'sbg:y': -347
+    'sbg:x': -635
+    'sbg:y': -176
   - id: msin
     type: 'Directory[]'
-    'sbg:x': -656
-    'sbg:y': -525
+    'sbg:x': -828
+    'sbg:y': -600
   - id: skymodels
     type: Directory
-    'sbg:x': -175.89886474609375
-    'sbg:y': -724.5
+    'sbg:x': 5
+    'sbg:y': -819
+  - id: min_amplitude_to_flag
+    type: float
+    'sbg:x': -798
+    'sbg:y': -441
+  - id: memoryperc
+    type: int
+    'sbg:x': -643
+    'sbg:y': -357
+  - id: baselines_to_flag
+    type: 'string[]'
+    'sbg:x': -448
+    'sbg:y': -161
+  - id: uvw
+    type: File?
+    'sbg:x': -360
+    'sbg:y': -851
+  - id: strategy
+    type: File?
+    'sbg:x': -430
+    'sbg:y': -713
+  - id: propagate_solutions
+    type: boolean
+    'sbg:x': -99
+    'sbg:y': -698
+  - id: flagunconverged
+    type: boolean
+    'sbg:x': -167
+    'sbg:y': -396
+  - id: do_smooth
+    type: boolean
+    'sbg:x': -201
+    'sbg:y': -237
 outputs:
   - id: outh5parm
     outputSource:
@@ -28,17 +60,27 @@ outputs:
     type: File
     'sbg:x': 477
     'sbg:y': -546.076171875
+  - id: log
+    outputSource:
+      - h5parm_collector/log
+    type: File
+    'sbg:x': 430.1015625
+    'sbg:y': -349.5
 steps:
   - id: ndppp_prep_cal
     in:
       - id: baselines_to_flag
         default: []
+        source:
+          - baselines_to_flag
       - id: elevation_to_flag
         default: 0deg..20deg
       - id: min_amplitude_to_flag
         default: 1.e-30
+        source: min_amplitude_to_flag
       - id: memoryperc
         default: 20
+        source: memoryperc
       - id: raw_data
         source: raw_data
       - id: demix
@@ -61,6 +103,10 @@ steps:
       - id: msin
         source:
           - ndppp_prep_cal/msout
+      - id: strategy
+        source: strategy
+      - id: uvw
+        source: uvw
     out:
       - id: output_ms
     run: ../steps/AOFlagger.cwl
@@ -74,6 +120,12 @@ steps:
         source: aoflagger/output_ms
       - id: skymodels
         source: skymodels
+      - id: flagunconverged
+        source: flagunconverged
+      - id: propagate_solutions
+        source: propagate_solutions
+      - id: do_smooth
+        source: do_smooth
     out:
       - id: h5parm
       - id: msout
@@ -88,8 +140,15 @@ steps:
       - id: h5parmFiles
         source:
           - calib_cal/h5parm
+      - id: squeeze
+        default: true
+      - id: verbose
+        default: true
+      - id: clobber
+        default: true
     out:
       - id: outh5parm
+      - id: log
     run: ../steps/H5ParmCollector.cwl
     label: H5parm_collector
     'sbg:x': 292.1979675292969