diff --git a/prefactor_calibrator.cwl b/prefactor_calibrator.cwl
index 324b62af8456672fb877b977620b6416fe935abc..84f669ea469e5c4319a24236205c5b22e515a005 100644
--- a/prefactor_calibrator.cwl
+++ b/prefactor_calibrator.cwl
@@ -5,10 +5,6 @@ label: prefactor_calibrator
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- - id: msin
- type: 'Directory[]'
- 'sbg:x': -659.0313110351562
- 'sbg:y': -522.6085205078125
- id: raw_data
type: boolean
'sbg:x': -620
@@ -21,6 +17,10 @@ inputs:
type: Directory
'sbg:x': -154.39886474609375
'sbg:y': -775.5
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -656
+ 'sbg:y': -525
outputs:
- id: demix_parmdb
outputSource:
@@ -32,18 +32,12 @@ outputs:
items: Directory
'sbg:x': -67.85011291503906
'sbg:y': -356.76287841796875
- - id: output_models
- outputSource:
- - find_skymodel_cal_py/output_models
- type: File
- 'sbg:x': 348.60113525390625
- 'sbg:y': -696.5
- id: msout
outputSource:
- ddecal/msout
type: Directory
- 'sbg:x': 507
- 'sbg:y': -524
+ 'sbg:x': 647.890625
+ 'sbg:y': -570.5
steps:
- id: ndppp_prep_cal
in:
@@ -81,8 +75,10 @@ steps:
- id: output_ms
run: steps/AOFlagger.cwl
label: AOFlagger
- 'sbg:x': -82
- 'sbg:y': -571
+ scatter:
+ - msin
+ 'sbg:x': -112
+ 'sbg:y': -556
- id: find_skymodel_cal_py
in:
- id: msin
@@ -94,8 +90,8 @@ steps:
- id: output_models
run: steps/find_skymodel_cal.cwl
label: find_skymodel_cal.py
- 'sbg:x': 105
- 'sbg:y': -709
+ 'sbg:x': 109.70829772949219
+ 'sbg:y': -674.2916870117188
- id: blsmooth
in:
- id: msin
@@ -104,19 +100,28 @@ steps:
- id: msout
run: steps/blsmooth.cwl
label: BLsmooth
- scatter:
- - msin
'sbg:x': 112
'sbg:y': -522
- id: ddecal
+ in:
+ - id: msin
+ source: predict/msout
+ out:
+ - id: msout
+ run: steps/ddecal.cwl
+ 'sbg:x': 490
+ 'sbg:y': -575
+ - id: predict
in:
- id: msin
source: blsmooth/msout
+ - id: sources_db
+ source: find_skymodel_cal_py/output_models
out:
- id: msout
run: steps/predict.cwl
- 'sbg:x': 313
- 'sbg:y': -521
+ 'sbg:x': 273
+ 'sbg:y': -573
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
diff --git a/steps/ddecal.cwl b/steps/ddecal.cwl
index f582c6b844c2243940a56a4b2e45e7b3186dff72..629ba6470d872d6b8c15092744947dee972df7e0 100644
--- a/steps/ddecal.cwl
+++ b/steps/ddecal.cwl
@@ -13,17 +13,16 @@ hints:
dockerPull: prefactor
arguments:
- - steps=[solve]
- - solve.type=ddecal
- - solve.h5parm=h5parm
- - solve.mode=rotation+diagonal
- - solve.uvlambdamin=300
- - solve.maxiter=50
- - solve.nchan=1
- - solve.solint=1
- - solve.propagateconvergedonly=True
- - solve.flagdivergedonly=True
- - solve.tolerance=1.e-3
+ - steps=[ddecal]
+ - ddecal.mode=rotation+diagonal
+ - ddecal.uvlambdamin=300
+ - ddecal.maxiter=50
+ - ddecal.nchan=1
+ - ddecal.solint=1
+ - ddecal.propagateconvergedonly=True
+ - ddecal.flagdivergedonly=True
+ - ddecal.tolerance=1.e-3
+ - ddecal.usemodelcolumn=True
inputs:
- id: msin
@@ -35,11 +34,17 @@ inputs:
- id: msin_datacolumn
type: string
- default: SMOOTHED_DATA
+ default: DATA
doc: Input data Column
inputBinding:
prefix: msin.datacolumn=
separate: false
+ - id: output_name_h5parm
+ type: string
+ default: instrument.h5
+ inputBinding:
+ prefix: --ddecal.h5parm=
+ separate: false
- id: msout_name
type: string
doc: Output Measurement Set
@@ -47,15 +52,6 @@ inputs:
inputBinding:
prefix: msout=
separate: false
- - id: usemodelcolumn
- type: boolean
- default: false
- doc: |
- Use model column. The model column name can be specified
- with msin.modelcolumn (default MODEL_DATA)
- inputBinding:
- prefix: solve.usemodelcolumn=True
-
#--------------------
- id: flagunconverged
type: boolean
@@ -85,3 +81,9 @@ outputs:
type: Directory
outputBinding:
glob: $(inputs.msout_name=="."?inputs.msin:inputs.msout_name)
+
+ - id: h5parm
+ doc: Filename of output H5Parm (to be read by e.g. losoto)
+ type: File
+ outputBinding:
+ glob: $(inputs.output_name_h5parm)
\ No newline at end of file
diff --git a/steps/predict.cwl b/steps/predict.cwl
index 7810fc7994ef8ecd2bcb4eeb8f42eecd833b336d..44fbd8f9a1672ddf2d9fdca32c8423db292222fb 100644
--- a/steps/predict.cwl
+++ b/steps/predict.cwl
@@ -1,70 +1,71 @@
-#!/usr/bin/env cwl-runner
-
class: CommandLineTool
cwlVersion: v1.0
-id: ddecal
-baseCommand: [DPPP]
-
-requirements:
- InlineJavascriptRequirement: {}
-
- InitialWorkDirRequirement:
- listing:
- - entry: $(inputs.msin)
- writable: true
-
-hints:
- DockerRequirement:
- dockerPull: prefactor
-
-arguments:
- - steps=[predict]
- - predict.beammode=array_factor
- - predict.usechannelfreq=False
- - msout=.
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: predict
+baseCommand:
+ - DPPP
inputs:
- id: msin
type: Directory
- doc: Input Measurement Set
inputBinding:
- prefix: msin=
- separate: false
- - id: msin_datacolumn
+ position: 0
+ prefix: msin=
+ separate: false
+ doc: Input Measurement Set
+ - default: DATA
+ id: msin_datacolumn
type: string
- default: DATA
- doc: Input data Column
inputBinding:
- prefix: msin.datacolumn=
- separate: false
- - id: msout_datacolumn
+ position: 0
+ prefix: msin.datacolumn=
+ separate: false
+ doc: Input data Column
+ - default: MODEL_DATA
+ id: msout_datacolumn
type: string
- default: MODEL_DATA
inputBinding:
- prefix: msout.datacolumn=
- separate: false
+ position: 0
+ prefix: msout.datacolumn=
+ separate: false
- id: sources_db
- type: [File, Directory]
+ type: File
inputBinding:
+ position: 0
prefix: predict.sourcedb=
separate: false
- - id: sources
- type: string[]
- default: null
+ - default: null
+ id: sources
+ type: 'string[]'
inputBinding:
+ position: 0
prefix: predict.sources=
- valueFrom: "[$(self)]"
separate: false
itemSeparator: ','
- - id: usebeammodel
+ valueFrom: '[$(self)]'
+ - default: false
+ id: usebeammodel
type: boolean
- default: false
inputBinding:
+ position: 0
prefix: predict.usebeammodel=True
-
-
outputs:
- id: msout
doc: Output Measurement Set
type: Directory
outputBinding:
glob: $(inputs.msin.basename)
+arguments:
+ - 'steps=[predict]'
+ - predict.beammode=array_factor
+ - predict.usechannelfreq=False
+ - msout=.
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
+ - class: InlineJavascriptRequirement
+hints:
+ - class: DockerRequirement
+ dockerPull: prefactor