diff --git a/steps/H5ParmCollector.cwl b/steps/H5ParmCollector.cwl
index 2849c64868f47ec7db5112c3e81483273bb0c696..89432c05a9b1d1c170182891b7b05cfeee5bbc10 100755
--- a/steps/H5ParmCollector.cwl
+++ b/steps/H5ParmCollector.cwl
@@ -1,36 +1,61 @@
-#!/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
diff --git a/steps/blsmooth.cwl b/steps/blsmooth.cwl
index 2f0d5ebbf74a243e9575254084c065bf0640fd31..9d0c5dbb9c65f0b119a745b75894fb04f7131eb3 100644
--- a/steps/blsmooth.cwl
+++ b/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
diff --git a/steps/ddecal.cwl b/steps/ddecal.cwl
index 9a5053b9d290b64fa6de5a9d26cc7ae307c2aae5..17830c4c3108231f45f9092f55eae9192dbe2439 100644
--- a/steps/ddecal.cwl
+++ b/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
diff --git a/subworkflow/calib_cal.cwl b/subworkflow/calib_cal.cwl
index c4427e8668031034af51865968df8baf1ead446c..926c40e4f362731eceb5f033225bae875c5d3bb6 100644
--- a/subworkflow/calib_cal.cwl
+++ b/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: []
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index 084e4c9f0b976c9300af030d62135adaf11deeee..bd5f299b4b7ae640770d018b5c20495dfd1a4f72 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/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