From 652f97c43a7b87f020a90cabfc5f1ef3595d4419 Mon Sep 17 00:00:00 2001
From: alex <alex@tls-tautenburg.de>
Date: Thu, 2 Sep 2021 09:58:48 +0000
Subject: [PATCH] Shallow listing
Former-commit-id: b7e75b3ca90d62fabc1f25deb537ca4cdf8f435e
---
.gitlab-ci.yml | 6 +-
lofar-cwl/steps/AOFlagger.cwl | 2 +-
lofar-cwl/steps/Ateamclipper.cwl | 4 +-
.../steps/DP3.AOFlaggerStepGenerator.cwl | 2 +-
.../steps/DP3.ApplyBeamStepGenerator.cwl | 2 +-
lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl | 2 +-
lofar-cwl/steps/DP3.AveragerStepGenerator.cwl | 2 +-
lofar-cwl/steps/DP3.DemixerStepGenerator.cwl | 2 +-
lofar-cwl/steps/DP3.EmptyParsetGenerator.cwl | 2 +-
lofar-cwl/steps/DP3.Execute.cwl | 2 +-
lofar-cwl/steps/DP3.FilterStepGenerator.cwl | 2 +-
lofar-cwl/steps/DP3.GenericStep.cwl | 2 +-
lofar-cwl/steps/DP3.ParsetGenerator.cwl | 2 +-
.../steps/DP3.PreflaggerStepGenerator.cwl | 2 +-
lofar-cwl/steps/DP3.Selector.cwl | 2 +-
lofar-cwl/steps/DPPP.cwl | 2 +-
lofar-cwl/steps/DirSelector.cwl | 2 +-
lofar-cwl/steps/FileSelector.cwl | 2 +-
lofar-cwl/steps/H5ParmCollector.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Abs.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Clip.cwl | 2 +-
lofar-cwl/steps/LoSoTo.ClockTec.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Duplicate.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Faraday.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Flag.cwl | 2 +-
lofar-cwl/steps/LoSoTo.FlagStation.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Flagextend.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Interpolate.cwl | 5 +-
lofar-cwl/steps/LoSoTo.Lofarbeam.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Norm.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Plot.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Polalign.cwl | 2 +-
lofar-cwl/steps/LoSoTo.PrefactorBandpass.cwl | 2 +-
lofar-cwl/steps/LoSoTo.PrefactorXYoffset.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Reset.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Residual.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Reweight.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Smooth.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Splitleak.cwl | 2 +-
lofar-cwl/steps/LoSoTo.Structure.cwl | 2 +-
lofar-cwl/steps/applybeam.cwl | 2 +-
lofar-cwl/steps/applycal.cwl | 2 +-
lofar-cwl/steps/applytarget.cwl | 2 +-
lofar-cwl/steps/average.cwl | 2 +-
lofar-cwl/steps/calib_rot_diag.cwl | 2 +-
lofar-cwl/steps/ddecal.cwl | 18 +-
lofar-cwl/steps/dpppconcat.cwl | 16 +-
lofar-cwl/steps/filter_predict.cwl | 22 +-
lofar-cwl/steps/gaincal.cwl | 28 +-
lofar-cwl/steps/interpolate_visibilities.cwl | 2 +-
lofar-cwl/steps/makesourcedb.cwl | 4 +-
lofar-cwl/steps/ms_concat.cwl | 2 +-
lofar-cwl/steps/predict.cwl | 16 +-
lofar-cwl/steps/wsclean.cwl | 2 +-
myworkflow.cwl | 2 +-
steps/add_missing_stations.cwl | 2 +-
steps/aoflag.cwl | 6 +-
steps/blsmooth.cwl | 21 +-
steps/bulk_rename.cwl | 2 +-
steps/check_ateam_separation.cwl | 6 +-
steps/check_unflagged_fraction.cwl | 4 +-
steps/collectlog.cwl | 2 +-
steps/compare_station_list.cwl | 6 +-
steps/concatenate_files.cwl | 2 +-
steps/createRMh5parm.cwl | 26 +-
steps/create_workflow_input.cwl | 2 +-
steps/directory_listing.cwl | 2 +-
steps/dppp_make_parset_cal.cwl | 117 ++++
steps/dppp_make_parset_target.cwl | 166 ++++++
steps/dppp_prep_cal.cwl | 103 ++++
steps/dppp_prep_target.cwl | 141 +++++
steps/filter_ms_group.cwl | 4 +-
steps/findRefAnt.cwl | 4 +-
steps/findRefAnt_join.cwl | 6 +-
steps/find_skymodel_cal.cwl | 4 +-
steps/find_skymodel_target.cwl | 7 +-
steps/get_targetname.cwl | 2 +-
steps/h5parm_pointingname.cwl | 2 +-
steps/h5parmcat.cwl | 2 +-
steps/identify_bad_antennas.cwl | 4 +-
steps/identify_bad_antennas_join.cwl | 4 +-
steps/merge_array.cwl | 2 +-
steps/merge_array_files.cwl | 2 +-
steps/plot_Ateamclipper.cwl | 2 +-
steps/plot_unflagged.cwl | 4 +-
steps/read_surl_list.cwl | 2 +-
steps/selectfirstdirectory.cwl | 3 +-
steps/selectfirstfile.cwl | 2 +-
steps/separate_results_directory.cwl | 2 +-
steps/sort_times_into_freqGroups.cwl | 7 +-
steps/stage.cwl | 2 +-
steps/structure_function.cwl | 2 +-
steps/summary.cwl | 2 +-
steps/surl_copy.cwl | 2 +-
steps/transfer_solutions.cwl | 2 +-
steps/untar.cwl | 2 +-
steps/uvplot.cwl | 2 +-
subworkflow/apply_calibrate_bp.cwl | 11 +-
subworkflow/apply_calibrate_fr.cwl | 11 +-
subworkflow/apply_calibrate_pa.cwl | 11 +-
subworkflow/apply_calibration.cwl | 2 +-
subworkflow/bandpass.cwl | 9 +-
subworkflow/calib_cal.cwl | 3 +-
subworkflow/calib_targ.cwl | 8 +-
subworkflow/clocktec.cwl | 6 +-
subworkflow/concat.cwl | 16 +-
subworkflow/faraday_rotation.cwl | 3 +-
subworkflow/ionosphere.cwl | 5 +-
subworkflow/losoto_bandpass.cwl | 6 +-
subworkflow/losoto_ion.cwl | 5 +-
subworkflow/ndppp_prep_cal.cwl | 346 ++++--------
subworkflow/ndppp_prep_targ.cwl | 510 +++++++-----------
subworkflow/pol_align.cwl | 2 +-
subworkflow/predict_calibrate.cwl | 11 +-
subworkflow/prep_target_applycal.cwl | 2 +-
subworkflow/smooth_calibrate.cwl | 2 +-
test_scatter/1st-tool.cwl | 2 +-
test_scatter/cat.cwl | 2 +-
test_scatter/scatter-workflow.cwl | 2 +-
test_scatter/scattertest.cwl | 2 +-
test_scatter/two_files.cwl | 2 +-
test_workflow/flag_average.cwl | 2 +-
test_workflow/two_steps.cwl | 2 +-
workflows/HBA_calibrator.cwl | 7 +-
workflows/HBA_target.cwl | 16 +-
...owload_surl_and_create_input_file-json.cwl | 2 +-
workflows/prefactor_calibrator.cwl | 7 +-
workflows/prefactor_calibrator/bp.cwl | 23 +-
workflows/prefactor_calibrator/fr.cwl | 5 +-
workflows/prefactor_calibrator/ion.cwl | 20 +-
workflows/prefactor_calibrator/pa.cwl | 5 +-
workflows/prefactor_calibrator/prep.cwl | 61 ++-
workflows/prefactor_target.cwl | 18 +-
workflows/prefactor_target/finalize.cwl | 37 +-
workflows/prefactor_target/gsmcal.cwl | 36 +-
workflows/prefactor_target/prep.cwl | 78 +--
137 files changed, 1275 insertions(+), 923 deletions(-)
create mode 100755 steps/dppp_make_parset_cal.cwl
create mode 100755 steps/dppp_make_parset_target.cwl
create mode 100755 steps/dppp_prep_cal.cwl
create mode 100755 steps/dppp_prep_target.cwl
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 78127616..6c18e444 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -65,6 +65,6 @@ run_hba_full:
script:
- cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH workflows/HBA_calibrator.cwl test_jobs/HBA_calibrator.json
- test_jobs/check_workflow_results.py results /builds/eosc/prefactor3-cwl/data/results_calibrator
-# - rm -rf results
-# - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH workflows/HBA_target.cwl test_jobs/HBA_target.json
-# - test_jobs/check_workflow_results.py results /builds/eosc/prefactor3-cwl/data/results_target
+ - rm -rf results
+ - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH workflows/HBA_target.cwl test_jobs/HBA_target.json
+ - test_jobs/check_workflow_results.py results /builds/eosc/prefactor3-cwl/data/results_target
diff --git a/lofar-cwl/steps/AOFlagger.cwl b/lofar-cwl/steps/AOFlagger.cwl
index fb45f040..5be41d5e 100644
--- a/lofar-cwl/steps/AOFlagger.cwl
+++ b/lofar-cwl/steps/AOFlagger.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: aoflagger
requirements:
diff --git a/lofar-cwl/steps/Ateamclipper.cwl b/lofar-cwl/steps/Ateamclipper.cwl
index 0badc835..e7799b54 100755
--- a/lofar-cwl/steps/Ateamclipper.cwl
+++ b/lofar-cwl/steps/Ateamclipper.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: check_ateam_separation
@@ -21,7 +21,7 @@ outputs:
outputBinding:
glob: $(inputs.msin.basename)
- id: logfile
- type: 'File[]'
+ type: File[]
outputBinding:
glob: Ateamclipper.log
- id: output
diff --git a/lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl b/lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl
index 2a70f602..a708ec86 100755
--- a/lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: aoflagger_step_generator
inputs:
diff --git a/lofar-cwl/steps/DP3.ApplyBeamStepGenerator.cwl b/lofar-cwl/steps/DP3.ApplyBeamStepGenerator.cwl
index 3e0c9fde..cf339a9a 100755
--- a/lofar-cwl/steps/DP3.ApplyBeamStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.ApplyBeamStepGenerator.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: applybeam_step_generator
inputs:
diff --git a/lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl b/lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
index 2850b977..2ba76d2a 100755
--- a/lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: applycal_step_generator
inputs:
diff --git a/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl b/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
index 47861182..13f6fb8a 100755
--- a/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: average_step_generator
inputs:
diff --git a/lofar-cwl/steps/DP3.DemixerStepGenerator.cwl b/lofar-cwl/steps/DP3.DemixerStepGenerator.cwl
index c88bdd17..c7b68cd9 100755
--- a/lofar-cwl/steps/DP3.DemixerStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.DemixerStepGenerator.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: demix_step_generator
diff --git a/lofar-cwl/steps/DP3.EmptyParsetGenerator.cwl b/lofar-cwl/steps/DP3.EmptyParsetGenerator.cwl
index f3e2c175..73aedd08 100755
--- a/lofar-cwl/steps/DP3.EmptyParsetGenerator.cwl
+++ b/lofar-cwl/steps/DP3.EmptyParsetGenerator.cwl
@@ -1,6 +1,6 @@
#!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.1
class: CommandLineTool
id: empty_parset_generator
baseCommand: [echo, 'steps=[]']
diff --git a/lofar-cwl/steps/DP3.Execute.cwl b/lofar-cwl/steps/DP3.Execute.cwl
index a1802137..ed3af2da 100644
--- a/lofar-cwl/steps/DP3.Execute.cwl
+++ b/lofar-cwl/steps/DP3.Execute.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: dp3_execute
label: DP3.Execute
$namespaces:
diff --git a/lofar-cwl/steps/DP3.FilterStepGenerator.cwl b/lofar-cwl/steps/DP3.FilterStepGenerator.cwl
index 0a582b27..0b21b047 100644
--- a/lofar-cwl/steps/DP3.FilterStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.FilterStepGenerator.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: dp3-filter-step-generator
diff --git a/lofar-cwl/steps/DP3.GenericStep.cwl b/lofar-cwl/steps/DP3.GenericStep.cwl
index 3c1a3031..a12bb7f0 100755
--- a/lofar-cwl/steps/DP3.GenericStep.cwl
+++ b/lofar-cwl/steps/DP3.GenericStep.cwl
@@ -1,6 +1,6 @@
#!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.1
class: ExpressionTool
id: generic_step
diff --git a/lofar-cwl/steps/DP3.ParsetGenerator.cwl b/lofar-cwl/steps/DP3.ParsetGenerator.cwl
index 123fdf1e..19fcd5a0 100644
--- a/lofar-cwl/steps/DP3.ParsetGenerator.cwl
+++ b/lofar-cwl/steps/DP3.ParsetGenerator.cwl
@@ -1,6 +1,6 @@
#!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.1
class: CommandLineTool
id: generic_step
diff --git a/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl b/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
index 64cd8515..94e2113b 100755
--- a/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: preflag_step_generator
inputs:
diff --git a/lofar-cwl/steps/DP3.Selector.cwl b/lofar-cwl/steps/DP3.Selector.cwl
index b50754a8..7876f347 100755
--- a/lofar-cwl/steps/DP3.Selector.cwl
+++ b/lofar-cwl/steps/DP3.Selector.cwl
@@ -1,5 +1,5 @@
class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: selector
inputs:
- id: select_a
diff --git a/lofar-cwl/steps/DPPP.cwl b/lofar-cwl/steps/DPPP.cwl
index de2ca5c7..40e8ccc0 100755
--- a/lofar-cwl/steps/DPPP.cwl
+++ b/lofar-cwl/steps/DPPP.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: dppp
diff --git a/lofar-cwl/steps/DirSelector.cwl b/lofar-cwl/steps/DirSelector.cwl
index d5bd0403..73a37b12 100644
--- a/lofar-cwl/steps/DirSelector.cwl
+++ b/lofar-cwl/steps/DirSelector.cwl
@@ -1,5 +1,5 @@
class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: dirselector
inputs:
- id: inputs
diff --git a/lofar-cwl/steps/FileSelector.cwl b/lofar-cwl/steps/FileSelector.cwl
index f935adca..8afb9365 100644
--- a/lofar-cwl/steps/FileSelector.cwl
+++ b/lofar-cwl/steps/FileSelector.cwl
@@ -1,5 +1,5 @@
class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: fileselector
inputs:
- id: inputs
diff --git a/lofar-cwl/steps/H5ParmCollector.cwl b/lofar-cwl/steps/H5ParmCollector.cwl
index 282c7e49..923d9e01 100755
--- a/lofar-cwl/steps/H5ParmCollector.cwl
+++ b/lofar-cwl/steps/H5ParmCollector.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
diff --git a/lofar-cwl/steps/LoSoTo.Abs.cwl b/lofar-cwl/steps/LoSoTo.Abs.cwl
index 4063c788..c8254164 100755
--- a/lofar-cwl/steps/LoSoTo.Abs.cwl
+++ b/lofar-cwl/steps/LoSoTo.Abs.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_abs
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.Clip.cwl b/lofar-cwl/steps/LoSoTo.Clip.cwl
index c829143c..c929b997 100644
--- a/lofar-cwl/steps/LoSoTo.Clip.cwl
+++ b/lofar-cwl/steps/LoSoTo.Clip.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_clip
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.ClockTec.cwl b/lofar-cwl/steps/LoSoTo.ClockTec.cwl
index 24b16e17..9f19b287 100644
--- a/lofar-cwl/steps/LoSoTo.ClockTec.cwl
+++ b/lofar-cwl/steps/LoSoTo.ClockTec.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_clocktec
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.Duplicate.cwl b/lofar-cwl/steps/LoSoTo.Duplicate.cwl
index a62ffbde..2c4937ec 100644
--- a/lofar-cwl/steps/LoSoTo.Duplicate.cwl
+++ b/lofar-cwl/steps/LoSoTo.Duplicate.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_duplicate
doc: |
diff --git a/lofar-cwl/steps/LoSoTo.Faraday.cwl b/lofar-cwl/steps/LoSoTo.Faraday.cwl
index aca07b95..fb5d2bf1 100644
--- a/lofar-cwl/steps/LoSoTo.Faraday.cwl
+++ b/lofar-cwl/steps/LoSoTo.Faraday.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_faraday
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.Flag.cwl b/lofar-cwl/steps/LoSoTo.Flag.cwl
index 2cfd5a6a..b4c2981a 100644
--- a/lofar-cwl/steps/LoSoTo.Flag.cwl
+++ b/lofar-cwl/steps/LoSoTo.Flag.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_flag
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.FlagStation.cwl b/lofar-cwl/steps/LoSoTo.FlagStation.cwl
index 2cb7b617..86479c74 100644
--- a/lofar-cwl/steps/LoSoTo.FlagStation.cwl
+++ b/lofar-cwl/steps/LoSoTo.FlagStation.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_flagstation
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.Flagextend.cwl b/lofar-cwl/steps/LoSoTo.Flagextend.cwl
index 4fd0a4c6..2e34c03a 100644
--- a/lofar-cwl/steps/LoSoTo.Flagextend.cwl
+++ b/lofar-cwl/steps/LoSoTo.Flagextend.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_flagextend
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.Interpolate.cwl b/lofar-cwl/steps/LoSoTo.Interpolate.cwl
index 113a938d..cbcede11 100644
--- a/lofar-cwl/steps/LoSoTo.Interpolate.cwl
+++ b/lofar-cwl/steps/LoSoTo.Interpolate.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_interpolate
$namespaces:
@@ -52,8 +52,9 @@ inputs:
type: string
doc: Output sol tab name
- id: newdelta
- type: string
+ type: string?
doc: Fundamental width between samples after regridding. E.g., "100kHz" or "10s"
+ default: "100kHz"
- id: delta
type: string?
diff --git a/lofar-cwl/steps/LoSoTo.Lofarbeam.cwl b/lofar-cwl/steps/LoSoTo.Lofarbeam.cwl
index 78cdb67f..e6b7fa9d 100644
--- a/lofar-cwl/steps/LoSoTo.Lofarbeam.cwl
+++ b/lofar-cwl/steps/LoSoTo.Lofarbeam.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_lofarbeam
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.Norm.cwl b/lofar-cwl/steps/LoSoTo.Norm.cwl
index 01a4634f..4ea38f4f 100644
--- a/lofar-cwl/steps/LoSoTo.Norm.cwl
+++ b/lofar-cwl/steps/LoSoTo.Norm.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_abs
doc: |
diff --git a/lofar-cwl/steps/LoSoTo.Plot.cwl b/lofar-cwl/steps/LoSoTo.Plot.cwl
index dcc7b02a..61d9b09a 100644
--- a/lofar-cwl/steps/LoSoTo.Plot.cwl
+++ b/lofar-cwl/steps/LoSoTo.Plot.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_plot
doc: |
diff --git a/lofar-cwl/steps/LoSoTo.Polalign.cwl b/lofar-cwl/steps/LoSoTo.Polalign.cwl
index 33e23bb7..1d3be1a7 100755
--- a/lofar-cwl/steps/LoSoTo.Polalign.cwl
+++ b/lofar-cwl/steps/LoSoTo.Polalign.cwl
@@ -1,6 +1,6 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_polalign
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.PrefactorBandpass.cwl b/lofar-cwl/steps/LoSoTo.PrefactorBandpass.cwl
index e480374d..ac46bdf9 100644
--- a/lofar-cwl/steps/LoSoTo.PrefactorBandpass.cwl
+++ b/lofar-cwl/steps/LoSoTo.PrefactorBandpass.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
diff --git a/lofar-cwl/steps/LoSoTo.PrefactorXYoffset.cwl b/lofar-cwl/steps/LoSoTo.PrefactorXYoffset.cwl
index b4b87b1d..ec6e1c14 100644
--- a/lofar-cwl/steps/LoSoTo.PrefactorXYoffset.cwl
+++ b/lofar-cwl/steps/LoSoTo.PrefactorXYoffset.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
diff --git a/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl b/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl
index 7d00a0c6..1d66ef65 100644
--- a/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl
+++ b/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_replicate_on_axis
doc: |
diff --git a/lofar-cwl/steps/LoSoTo.Reset.cwl b/lofar-cwl/steps/LoSoTo.Reset.cwl
index 81bf21dd..57017910 100644
--- a/lofar-cwl/steps/LoSoTo.Reset.cwl
+++ b/lofar-cwl/steps/LoSoTo.Reset.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_reset
doc: Subtract/divide two tables or a clock/tec/tec3rd/rm from a phase.
diff --git a/lofar-cwl/steps/LoSoTo.Residual.cwl b/lofar-cwl/steps/LoSoTo.Residual.cwl
index 21f451c9..26ae49cd 100644
--- a/lofar-cwl/steps/LoSoTo.Residual.cwl
+++ b/lofar-cwl/steps/LoSoTo.Residual.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_residual
doc: Subtract/divide two tables or a clock/tec/tec3rd/rm from a phase.
diff --git a/lofar-cwl/steps/LoSoTo.Reweight.cwl b/lofar-cwl/steps/LoSoTo.Reweight.cwl
index b0d274ff..8df7c046 100644
--- a/lofar-cwl/steps/LoSoTo.Reweight.cwl
+++ b/lofar-cwl/steps/LoSoTo.Reweight.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_reweight
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.Smooth.cwl b/lofar-cwl/steps/LoSoTo.Smooth.cwl
index f07e29e5..29ab625b 100644
--- a/lofar-cwl/steps/LoSoTo.Smooth.cwl
+++ b/lofar-cwl/steps/LoSoTo.Smooth.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_smooth
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.Splitleak.cwl b/lofar-cwl/steps/LoSoTo.Splitleak.cwl
index 27004fb4..5e16f93c 100644
--- a/lofar-cwl/steps/LoSoTo.Splitleak.cwl
+++ b/lofar-cwl/steps/LoSoTo.Splitleak.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_splitleak
$namespaces:
diff --git a/lofar-cwl/steps/LoSoTo.Structure.cwl b/lofar-cwl/steps/LoSoTo.Structure.cwl
index e8ba30ca..4a54161f 100644
--- a/lofar-cwl/steps/LoSoTo.Structure.cwl
+++ b/lofar-cwl/steps/LoSoTo.Structure.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_structure
$namespaces:
diff --git a/lofar-cwl/steps/applybeam.cwl b/lofar-cwl/steps/applybeam.cwl
index b2a1fb6b..14e02ccb 100644
--- a/lofar-cwl/steps/applybeam.cwl
+++ b/lofar-cwl/steps/applybeam.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: applybeam
diff --git a/lofar-cwl/steps/applycal.cwl b/lofar-cwl/steps/applycal.cwl
index 1a0fa547..7ab1a0de 100644
--- a/lofar-cwl/steps/applycal.cwl
+++ b/lofar-cwl/steps/applycal.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: applycal
diff --git a/lofar-cwl/steps/applytarget.cwl b/lofar-cwl/steps/applytarget.cwl
index 33cee0a3..3ec0fdd3 100644
--- a/lofar-cwl/steps/applytarget.cwl
+++ b/lofar-cwl/steps/applytarget.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: applytarget
diff --git a/lofar-cwl/steps/average.cwl b/lofar-cwl/steps/average.cwl
index deb84466..06f5e0b7 100644
--- a/lofar-cwl/steps/average.cwl
+++ b/lofar-cwl/steps/average.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: average
diff --git a/lofar-cwl/steps/calib_rot_diag.cwl b/lofar-cwl/steps/calib_rot_diag.cwl
index a167095c..fd35fe5c 100644
--- a/lofar-cwl/steps/calib_rot_diag.cwl
+++ b/lofar-cwl/steps/calib_rot_diag.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
diff --git a/lofar-cwl/steps/ddecal.cwl b/lofar-cwl/steps/ddecal.cwl
index 43ed10b9..4f1a9c39 100644
--- a/lofar-cwl/steps/ddecal.cwl
+++ b/lofar-cwl/steps/ddecal.cwl
@@ -1,7 +1,7 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: calib_rot_diag
baseCommand: [DPPP]
@@ -36,7 +36,7 @@ inputs:
separate: false
- id: msin_datacolumn
- type: string
+ type: string?
default: DATA
doc: Input data Column
inputBinding:
@@ -44,7 +44,7 @@ inputs:
separate: false
- id: msin_modelcolum
- type: string
+ type: string?
default: MODEL_DATA
doc: Model data Column
inputBinding:
@@ -52,13 +52,13 @@ inputs:
separate: false
- id: output_name_h5parm
- type: string
+ type: string?
default: instrument.h5
inputBinding:
prefix: ddecal.h5parm=
separate: false
- id: msout_name
- type: string
+ type: string?
doc: Output Measurement Set
default: "OUT.MS"
inputBinding:
@@ -67,12 +67,12 @@ inputs:
#--------------------
- id: propagate_solutions
- type: boolean
+ type: boolean?
default: true
inputBinding:
prefix: ddecal.propagatesolutions=True
- id: flagunconverged
- type: boolean
+ type: boolean?
default: false
doc: |
Flag unconverged solutions (i.e., those from solves that did not converge
@@ -81,7 +81,7 @@ inputs:
prefix: ddecal.flagdivergedonly=True
- id: flagdivergedonly
default: false
- type: boolean
+ type: boolean?
doc: |
Flag only the unconverged solutions for which divergence was detected.
At the moment, this option is effective only for rotation+diagonal
@@ -94,7 +94,7 @@ inputs:
inputBinding:
prefix: ddecal.flagdivergedonly=True
- id: storagemanager
- type: string
+ type: string?
default: ""
inputBinding:
prefix: msout.storagemanager=
diff --git a/lofar-cwl/steps/dpppconcat.cwl b/lofar-cwl/steps/dpppconcat.cwl
index 8fe2290c..9fd3604f 100644
--- a/lofar-cwl/steps/dpppconcat.cwl
+++ b/lofar-cwl/steps/dpppconcat.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: dpppconcat
@@ -26,7 +26,7 @@ inputs:
shellQuote: false
position: 0
- id: msin_datacolumn
- type: string
+ type: string?
inputBinding:
prefix: msin.datacolumn=
separate: false
@@ -35,7 +35,7 @@ inputs:
doc: Input data Column
default: DATA
- id: msout_datacolumn
- type: string
+ type: string?
inputBinding:
prefix: msout.datacolumn=
separate: false
@@ -43,7 +43,7 @@ inputs:
position: 0
default: DATA
- id: filter_baselines
- type: string
+ type: string?
inputBinding:
prefix: filter.baseline=
separate: false
@@ -52,28 +52,28 @@ inputs:
valueFrom: $(self)
default: null
- id: filter_remove
- type: boolean
+ type: boolean?
inputBinding:
prefix: filter.remove=True
shellQuote: false
position: 0
default: false
- id: writefullresflag
- type: boolean
+ type: boolean?
inputBinding:
prefix: msout.writefullresflag=True
shellQuote: false
position: 0
default: false
- id: overwrite
- type: boolean
+ type: boolean?
inputBinding:
prefix: msout.overwrite=True
shellQuote: false
position: 0
default: false
- id: storagemanager
- type: string
+ type: string?
inputBinding:
prefix: msout.storagemanager=
separate: false
diff --git a/lofar-cwl/steps/filter_predict.cwl b/lofar-cwl/steps/filter_predict.cwl
index 64a39c07..e069f929 100644
--- a/lofar-cwl/steps/filter_predict.cwl
+++ b/lofar-cwl/steps/filter_predict.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: predict
@@ -15,7 +15,7 @@ inputs:
doc: Input Measurement Set
- default: DATA
id: msin_datacolumn
- type: string
+ type: string?
inputBinding:
position: 0
prefix: msin.datacolumn=
@@ -23,7 +23,7 @@ inputs:
doc: Input data Column
- default: MODEL_DATA
id: msout_datacolumn
- type: string
+ type: string?
inputBinding:
position: 0
prefix: msout.datacolumn=
@@ -36,7 +36,7 @@ inputs:
separate: false
- default: null
id: sources
- type: 'string[]'
+ type: 'string[]?'
inputBinding:
position: 0
prefix: predict.sources=
@@ -45,19 +45,19 @@ inputs:
valueFrom: "[$(self.join(','))]"
- default: false
id: usebeammodel
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: predict.usebeammodel=True
- default: false
id: onebeamperpatch
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: predict.onebeamperpatch=True
- default: null
id: filter_baselines
- type: string
+ type: string?
inputBinding:
position: 0
prefix: filter.baseline=
@@ -65,22 +65,22 @@ inputs:
valueFrom: '$(self)'
- default: false
id: filter_remove
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: filter.remove=True
- id: writefullresflag
- type: boolean
+ type: boolean?
default: false
inputBinding:
prefix: msout.writefullresflag=True
- id: overwrite
- type: boolean
+ type: boolean?
default: false
inputBinding:
prefix: msout.overwrite=True
- id: storagemanager
- type: string
+ type: string?
default: ""
inputBinding:
prefix: msout.storagemanager=
diff --git a/lofar-cwl/steps/gaincal.cwl b/lofar-cwl/steps/gaincal.cwl
index e749346f..1cccdaef 100644
--- a/lofar-cwl/steps/gaincal.cwl
+++ b/lofar-cwl/steps/gaincal.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
@@ -41,14 +41,14 @@ inputs:
separate: false
- default: true
id: usebeammodel
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: gaincal.usebeammodel=true
separate: false
- default: 1
id: solint
- type: int
+ type: int?
doc: >
Number of time slots on which a solution is assumed to be constant (same
as CellSize.Time in BBS).
@@ -68,7 +68,7 @@ inputs:
doc: Input data Column
- default: false
id: onebeamperpatch
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: gaincal.onebeamperpatch=True
@@ -76,7 +76,7 @@ inputs:
doc: Input data Column
- default: MODEL_DATA
id: msin_modelcolum
- type: string
+ type: string?
inputBinding:
position: 0
prefix: msin.modelcolumn=
@@ -84,14 +84,14 @@ inputs:
doc: Model data Column
- default: instrument.h5
id: output_name_h5parm
- type: string
+ type: string?
inputBinding:
position: 0
prefix: gaincal.parmdb=
separate: false
- default: out.MS
id: msout_name
- type: string
+ type: string?
inputBinding:
position: 0
prefix: msout=
@@ -99,49 +99,49 @@ inputs:
doc: Output Measurement Set
- default: true
id: propagatesolutions
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: gaincal.propagatesolutions=True
separate: false
- default: true
id: usechannelfreq
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: gaincal.usechannelfreq=True
separate: false
- default: array_factor
id: beammode
- type: string
+ type: string?
inputBinding:
position: 0
prefix: gaincal.beammode=
separate: false
- default: 0
id: nchan
- type: int
+ type: int?
inputBinding:
position: 0
prefix: gaincal.nchan=
separate: false
- default: 50
id: maxiter
- type: int
+ type: int?
inputBinding:
position: 0
prefix: gaincal.maxiter=
separate: false
- default: 1e-3
id: tolerance
- type: float
+ type: float?
inputBinding:
position: 0
prefix: gaincal.tolerance=
separate: false
- default: null
id: blrange
- type: 'int[]'
+ type: 'int[]?'
inputBinding:
position: 0
prefix: filter.blrange=
diff --git a/lofar-cwl/steps/interpolate_visibilities.cwl b/lofar-cwl/steps/interpolate_visibilities.cwl
index bc9a36ee..78ad7078 100644
--- a/lofar-cwl/steps/interpolate_visibilities.cwl
+++ b/lofar-cwl/steps/interpolate_visibilities.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: interpolate_visibilities
diff --git a/lofar-cwl/steps/makesourcedb.cwl b/lofar-cwl/steps/makesourcedb.cwl
index 3a11c723..e92b2b0d 100755
--- a/lofar-cwl/steps/makesourcedb.cwl
+++ b/lofar-cwl/steps/makesourcedb.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: make_sourcedb
@@ -52,7 +52,7 @@ outputs:
outputBinding:
glob: $(inputs.output_file_name)
- id: log
- type: File?
+ type: File
outputBinding:
glob: $(inputs.logname)
label: make_sourcedb_ateam
diff --git a/lofar-cwl/steps/ms_concat.cwl b/lofar-cwl/steps/ms_concat.cwl
index 1ff03cbb..5b39b048 100644
--- a/lofar-cwl/steps/ms_concat.cwl
+++ b/lofar-cwl/steps/ms_concat.cwl
@@ -46,7 +46,7 @@ outputs:
outputBinding:
glob: 'workdir/out_*'
- id: logfile
- type: File?
+ type: File
outputBinding:
glob: ms_concat.log
label: ms_concat
diff --git a/lofar-cwl/steps/predict.cwl b/lofar-cwl/steps/predict.cwl
index fab5d2a5..44e5c96b 100644
--- a/lofar-cwl/steps/predict.cwl
+++ b/lofar-cwl/steps/predict.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: predict
@@ -15,7 +15,7 @@ inputs:
doc: Input Measurement Set
- default: DATA
id: msin_datacolumn
- type: string
+ type: string?
inputBinding:
position: 0
prefix: msin.datacolumn=
@@ -23,7 +23,7 @@ inputs:
doc: Input data Column
- default: MODEL_DATA
id: msout_datacolumn
- type: string
+ type: string?
inputBinding:
position: 0
prefix: msout.datacolumn=
@@ -36,7 +36,7 @@ inputs:
separate: false
- default: null
id: sources
- type: 'string[]'
+ type: 'string[]?'
inputBinding:
position: 0
prefix: predict.sources=
@@ -45,22 +45,22 @@ inputs:
valueFrom: '[$(self)]'
- default: false
id: usebeammodel
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: predict.usebeammodel=True
- id: writefullresflag
- type: boolean
+ type: boolean?
default: false
inputBinding:
prefix: msout.writefullresflag=True
- id: overwrite
- type: boolean
+ type: boolean?
default: false
inputBinding:
prefix: msout.overwrite=True
- id: storagemanager
- type: string
+ type: string?
default: ""
inputBinding:
prefix: msout.storagemanager=
diff --git a/lofar-cwl/steps/wsclean.cwl b/lofar-cwl/steps/wsclean.cwl
index bd070945..22e5dd97 100644
--- a/lofar-cwl/steps/wsclean.cwl
+++ b/lofar-cwl/steps/wsclean.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: wsclean
diff --git a/myworkflow.cwl b/myworkflow.cwl
index d3406ade..90e2d295 100755
--- a/myworkflow.cwl
+++ b/myworkflow.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: myworkflow
label: MyWorkflow
$namespaces:
diff --git a/steps/add_missing_stations.cwl b/steps/add_missing_stations.cwl
index 5370829b..9fb3c591 100644
--- a/steps/add_missing_stations.cwl
+++ b/steps/add_missing_stations.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
diff --git a/steps/aoflag.cwl b/steps/aoflag.cwl
index 4f6c03a5..04e259d1 100644
--- a/steps/aoflag.cwl
+++ b/steps/aoflag.cwl
@@ -1,11 +1,11 @@
#!/usr/bin/env cwl-runner
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: aoflagger
hints:
- DockerRequirement:
+ - class: DockerRequirement
dockerPull: lofareosc/prefactor3-cwl
baseCommand:
@@ -119,7 +119,7 @@ outputs:
outputBinding:
glob: 'workdir/out_*'
- id: logfile
- type: File?
+ type: File
outputBinding:
glob: aoflag.log
label: AOFlagger
diff --git a/steps/blsmooth.cwl b/steps/blsmooth.cwl
index 6f4efd6b..072d088e 100644
--- a/steps/blsmooth.cwl
+++ b/steps/blsmooth.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: blsmooth
label: BLsmooth
baseCommand:
@@ -12,13 +12,14 @@ inputs:
doc: Input measurement set
- default: 0.2
id: ionfactor
- type: float
+ type: float?
inputBinding:
position: 0
prefix: '-f'
doc: Gives an indication on how strong is the ionosphere
- id: do_smooth
- type: boolean
+ type: boolean?
+ default: true
doc: 'If true performs smoothing'
inputBinding:
prefix: -S
@@ -26,28 +27,28 @@ inputs:
separate: true
- default: 0.5
id: bscalefactor
- type: float
+ type: float?
inputBinding:
position: 0
prefix: '-s'
doc: Gives an indication on how the smoothing varies with
- default: DATA
id: in_column_name
- type: string
+ type: string?
inputBinding:
position: 0
prefix: '-i'
doc: Column name to smooth
- default: SMOOTHED_DATA
id: out_column
- type: string
+ type: string?
inputBinding:
position: 0
prefix: '-o'
doc: Output column
- default: false
id: weight
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: '-w'
@@ -56,21 +57,21 @@ inputs:
the MS!
- default: false
id: restore
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: '-r'
doc: If WEIGHT_SPECTRUM_ORIG exists then restore it before smoothing
- default: false
id: nobackup
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: '-b'
doc: Do not backup the old WEIGHT_SPECTRUM in WEIGHT_SPECTRUM_ORIG
- default: false
id: onlyamp
- type: boolean
+ type: boolean?
inputBinding:
position: 0
prefix: '-a'
diff --git a/steps/bulk_rename.cwl b/steps/bulk_rename.cwl
index 9102a16c..cb456fb8 100644
--- a/steps/bulk_rename.cwl
+++ b/steps/bulk_rename.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: bulk_rename
diff --git a/steps/check_ateam_separation.cwl b/steps/check_ateam_separation.cwl
index 911dfb45..32908f0e 100644
--- a/steps/check_ateam_separation.cwl
+++ b/steps/check_ateam_separation.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: check_ateam_separation
baseCommand:
- check_Ateam_separation.py
@@ -26,7 +26,7 @@ inputs:
outputs:
- id: output_imag
doc: Output image
- type: File?
+ type: File
outputBinding:
glob: $(inputs.output_image_name)
- id: output_json
@@ -35,7 +35,7 @@ outputs:
outputBinding:
glob: '*.json'
- id: logfile
- type: File?
+ type: File
outputBinding:
glob: Ateam_separation.log
label: check_Ateam_separation
diff --git a/steps/check_unflagged_fraction.cwl b/steps/check_unflagged_fraction.cwl
index 5790c430..3848b006 100644
--- a/steps/check_unflagged_fraction.cwl
+++ b/steps/check_unflagged_fraction.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: check_unflagged_fraction
@@ -56,7 +56,7 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).unflagged_fraction)
- id: logfile
- type: File[]?
+ type: File[]
outputBinding:
glob: 'check_unflagged_fraction*.log'
diff --git a/steps/collectlog.cwl b/steps/collectlog.cwl
index ab5987b1..b7dc32b3 100644
--- a/steps/collectlog.cwl
+++ b/steps/collectlog.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: collectlog
diff --git a/steps/compare_station_list.cwl b/steps/compare_station_list.cwl
index 7c1b5414..75e1f906 100644
--- a/steps/compare_station_list.cwl
+++ b/steps/compare_station_list.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: compare_station_list
@@ -51,7 +51,7 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).filter_out)
- id: logfile
- type: File[]?
+ type: File[]
outputBinding:
glob: 'compareStationList*.log'
@@ -59,7 +59,7 @@ requirements:
- class: InlineJavascriptRequirement
hints:
- DockerRequirement:
+ - class: DockerRequirement
dockerPull: lofareosc/prefactor3-cwl
stdout: compareStationList.log
stderr: compareStationList_err.log
\ No newline at end of file
diff --git a/steps/concatenate_files.cwl b/steps/concatenate_files.cwl
index e3f5bdac..3b874498 100644
--- a/steps/concatenate_files.cwl
+++ b/steps/concatenate_files.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: concatfiles
diff --git a/steps/createRMh5parm.cwl b/steps/createRMh5parm.cwl
index 06c98593..60de7379 100644
--- a/steps/createRMh5parm.cwl
+++ b/steps/createRMh5parm.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: createRMh5parm
label: createRMh5parm
baseCommand:
@@ -19,77 +19,77 @@ inputs:
position: 2
doc: Input h5parm solutions file
- id: ionex_server
- type: string
+ type: string?
doc: IONEX Server path
default: 'ftp://ftp.aiub.unibe.ch/CODE/'
inputBinding:
prefix: '--server'
position: 0
- id: ionex_prefix
- type: string
+ type: string?
doc: IONEX Prefix
default: 'CODG'
inputBinding:
prefix: '--prefix'
position: 0
- id: ionex_path
- type: string
+ type: string?
doc: IONEX path
default: './'
inputBinding:
prefix: '--path'
position: 0
- id: solset
- type: string
+ type: string?
doc: solset in which IONEX solution are put
default: 'sol000'
inputBinding:
prefix: '--solsetName'
position: 0
- id: timestep
- type: float
+ type: float?
doc: timestep in seconds
default: 300.
inputBinding:
prefix: '-t'
position: 0
- id: smart_interpol
- type: float
+ type: float?
doc: float parameter describing how much of Earth rotation is taken in to account in interpolation of the IONEX files. 1.0 means time interpolation assumes ionosphere rotates in opposite direction of the Earth
default: 0.
inputBinding:
prefix: '-e'
position: 0
- id: proxyserver
- type: string
+ type: string?
doc: Specify proxy server if necessary
default: null
inputBinding:
prefix: '--proxyserver'
position: 0
- id: proxyport
- type: int
+ type: int?
doc: Specify proxy port if necessary
default: null
inputBinding:
prefix: '--proxyport'
position: 0
- id: proxytype
- type: string
+ type: string?
doc: Specify proxy type if necessary
default: null
inputBinding:
prefix: '--proxytype'
position: 0
- id: proxyuser
- type: string
+ type: string?
doc: Specify proxy user name if necessary
default: null
inputBinding:
prefix: '--proxyuser'
position: 0
- id: proxypass
- type: string
+ type: string?
doc: Specify proxy server password if necessary
default: null
inputBinding:
@@ -113,7 +113,7 @@ hints:
listing:
- entry: $(inputs.h5parm)
writable: true
-
+
stdout: createh5parm.log
stderr: createh5parm_err.log
$namespaces:
diff --git a/steps/create_workflow_input.cwl b/steps/create_workflow_input.cwl
index 505eecf6..10b25bc5 100644
--- a/steps/create_workflow_input.cwl
+++ b/steps/create_workflow_input.cwl
@@ -3,7 +3,7 @@ $namespaces:
id: create_workflow_input
label: create_workflow_input
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
inputs:
- id: msin
type: Directory[]
diff --git a/steps/directory_listing.cwl b/steps/directory_listing.cwl
index 73301837..7c6763bf 100644
--- a/steps/directory_listing.cwl
+++ b/steps/directory_listing.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: directory_listing
diff --git a/steps/dppp_make_parset_cal.cwl b/steps/dppp_make_parset_cal.cwl
new file mode 100755
index 00000000..bb6fbfdd
--- /dev/null
+++ b/steps/dppp_make_parset_cal.cwl
@@ -0,0 +1,117 @@
+class: CommandLineTool
+cwlVersion: v1.1
+id: make_parset
+label: define_parset
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: raw_data
+ type: boolean?
+ default: false
+ - id: demix
+ type: boolean?
+ default: false
+ - id: filter_baselines
+ type: string?
+ default: '[CR]S*&'
+ - id: memoryperc
+ type: int?
+ default: 20
+ - id: baselines_to_flag
+ type: 'string[]?'
+ default: []
+ - id: elevation_to_flag
+ type: string?
+ default: '0deg..15deg'
+ - id: min_amplitude_to_flag
+ type: float?
+ default: 1e-30
+ - id: timeresolution
+ type: int?
+ default: 4
+ - id: freqresolution
+ type: string?
+ default: '48.82kHz'
+ - id: process_baselines_cal
+ type: string?
+ default: '*&'
+ - id: demix_timestep
+ type: int?
+ default: 10
+ - id: demix_freqstep
+ type: int?
+ default: 16
+ - id: target_source
+ type: string?
+ default: ''
+ - id: subtract_sources
+ type: 'string[]?'
+ default:
+ - CasA
+ - CygA
+ - id: ntimechunk
+ type: int?
+ default: 10
+outputs:
+ - id: output
+ type: File
+ outputBinding:
+ glob: DPPP.parset
+baseCommand:
+ - cp
+arguments:
+ - prefix: ''
+ shellQuote: false
+ position: 0
+ valueFrom: input.parset
+ - prefix: ''
+ shellQuote: false
+ position: 0
+ valueFrom: DPPP.parset
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: ShellCommandRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: input.parset
+ entry: |+
+ steps = [$(inputs.raw_data?'flagedge,aoflag,':'')flagbaseline,flagelev,flagamp,$(inputs.demix?'demix,':'')filter,avg]
+ #
+ msout.storagemanager = "Dysco"
+ msout.storagemanager.databitrate = 0
+ #
+ filter.type = filter
+ filter.baseline = $(inputs.filter_baselines)
+ filter.remove = true
+ #
+ flagedge.type = preflagger
+ flagedge.chan = [0..nchan/32-1,31*nchan/32..nchan-1]
+ #
+ aoflag.type = aoflagger
+ aoflag.memoryperc = $(inputs.memoryperc)
+ aoflag.keepstatistics = false
+ #
+ flagbaseline.type = preflagger
+ flagbaseline.baseline = $(inputs.baselines_to_flag)
+ #
+ flagelev.type = preflagger
+ flagelev.elevation = $(inputs.elevation_to_flag)
+ #
+ flagamp.type = preflagger
+ flagamp.amplmin = $(inputs.min_amplitude_to_flag)
+ #
+ avg.type = average
+ avg.timeresolution = $(inputs.timeresolution)
+ avg.freqresolution = $(inputs.freqresolution)
+ #
+ demix.type = demixer
+ demix.baseline = $(inputs.process_baselines_cal)
+ demix.demixfreqstep = $(inputs.demix_freqstep)
+ demix.demixtimestep = $(inputs.demix_timestep)
+ demix.ignoretarget = False
+ demix.targetsource = $(inputs.target_source)
+ demix.subtractsources = $(inputs.subtract_sources)
+ demix.ntimechunk = $(inputs.ntimechunk)
+ demix.freqstep = 1
+ demix.timestep = 1
+ demix.instrumentmodel = instrument
diff --git a/steps/dppp_make_parset_target.cwl b/steps/dppp_make_parset_target.cwl
new file mode 100755
index 00000000..f31c0a84
--- /dev/null
+++ b/steps/dppp_make_parset_target.cwl
@@ -0,0 +1,166 @@
+class: CommandLineTool
+cwlVersion: v1.1
+id: make_parset
+label: define_parset
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: raw_data
+ type: boolean?
+ default: false
+ - id: demix
+ type: boolean?
+ default: false
+ - id: apply_tec_correction
+ type: boolean?
+ default: false
+ - id: apply_rm_correction
+ type: boolean?
+ default: true
+ - id: apply_phase_correction
+ type: boolean?
+ default: false
+ - id: apply_clock_correction
+ type: boolean?
+ default: true
+ - id: apply_beam_correction
+ type: boolean?
+ default: true
+ - id: filter_baselines
+ type: string?
+ default: '[CR]S*&'
+ - id: memoryperc
+ type: int?
+ default: 20
+ - id: baselines_to_flag
+ type: 'string[]?'
+ default: []
+ - id: elevation_to_flag
+ type: string?
+ default: '0deg..15deg'
+ - id: min_amplitude_to_flag
+ type: float?
+ default: 1e-30
+ - id: updateweights
+ type: boolean?
+ default: true
+ - id: timeresolution
+ type: int?
+ default: 4
+ - id: freqresolution
+ type: string?
+ default: '48.82kHz'
+ - id: process_baselines_target
+ type: string?
+ default: '[CR]S*&'
+ - id: demix_timestep
+ type: int?
+ default: 10
+ - id: demix_freqstep
+ type: int?
+ default: 16
+ - id: target_source
+ type: string?
+ default: ''
+ - id: subtract_sources
+ type: 'string[]?'
+ default:
+ - CasA
+ - CygA
+ - id: ntimechunk
+ type: int?
+ default: 10
+outputs:
+ - id: output
+ type: File
+ outputBinding:
+ glob: DPPP.parset
+baseCommand:
+ - cp
+arguments:
+ - prefix: ''
+ shellQuote: false
+ position: 0
+ valueFrom: input.parset
+ - prefix: ''
+ shellQuote: false
+ position: 0
+ valueFrom: DPPP.parset
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: ShellCommandRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: input.parset
+ entry: |+
+ steps = [$(inputs.raw_data?'flagedge,aoflag,':'')flagbaseline,flagelev,flagamp,$(inputs.demix?'demix,':'')filter,applyPA,applybandpass,$(inputs.apply_clock_correction?'applyclock,':'')$(inputs.apply_beam_correction?'applybeam,':'')$(inputs.apply_rm_correction?'applyRM,':'')$(inputs.apply_tec_correction?'applytec,':'')$(inputs.apply_phase_correction?'applyphase,':'')avg]
+ #
+ msout.storagemanager = "Dysco"
+ msout.storagemanager.databitrate = 0
+ #
+ filter.type = filter
+ filter.baseline = $(inputs.filter_baselines)
+ filter.remove = true
+ #
+ flagedge.type = preflagger
+ flagedge.chan = [0..nchan/32-1,31*nchan/32..nchan-1]
+ #
+ aoflag.type = aoflagger
+ aoflag.memoryperc = $(inputs.memoryperc)
+ aoflag.keepstatistics = false
+ #
+ flagbaseline.type = preflagger
+ flagbaseline.baseline = $(inputs.baselines_to_flag)
+ #
+ flagelev.type = preflagger
+ flagelev.elevation = $(inputs.elevation_to_flag)
+ #
+ flagamp.type = preflagger
+ flagamp.amplmin = $(inputs.min_amplitude_to_flag)
+ #
+ applyPA.type = applycal
+ applyPA.correction = polalign
+ applyPA.solset = calibrator
+ #
+ applybandpass.type = applycal
+ applybandpass.correction = bandpass
+ applybandpass.updateweights = $(inputs.updateweights?'True':'False')
+ applybandpass.solset = calibrator
+ #
+ applyclock.type = applycal
+ applyclock.correction = clock
+ applyclock.solset = calibrator
+ #
+ applytec.type = applycal
+ applytec.correction = tec
+ applytec.solset = calibrator
+ #
+ applyphase.type = applycal
+ applyphase.correction = phaseOrig
+ applyphase.solset = calibrator
+ #
+ applyRM.type = applycal
+ applyRM.correction = RMextract
+ applyRM.solset = target
+ #
+ applybeam.type = applybeam
+ applybeam.usechannelfreq = True
+ applybeam.updateweights = $(inputs.updateweights?'True':'False')
+ applybeam.invert = True
+ applybeam.beammode = element
+ #
+ avg.type = average
+ avg.timeresolution = $(inputs.timeresolution)
+ avg.freqresolution = $(inputs.freqresolution)
+ #
+ demix.type = demixer
+ demix.baseline = $(inputs.process_baselines_target)
+ demix.demixfreqstep = $(inputs.demix_freqstep)
+ demix.demixtimestep = $(inputs.demix_timestep)
+ demix.ignoretarget = False
+ demix.targetsource = $(inputs.target_source)
+ demix.subtractsources = $(inputs.subtract_sources)
+ demix.ntimechunk = $(inputs.ntimechunk)
+ demix.freqstep = 1
+ demix.timestep = 1
+ demix.instrumentmodel = instrument
diff --git a/steps/dppp_prep_cal.cwl b/steps/dppp_prep_cal.cwl
new file mode 100755
index 00000000..e8d9dda6
--- /dev/null
+++ b/steps/dppp_prep_cal.cwl
@@ -0,0 +1,103 @@
+class: CommandLineTool
+cwlVersion: v1.1
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: dppp
+baseCommand:
+ - DP3
+inputs:
+ - id: parset
+ type: File?
+ inputBinding:
+ position: -1
+ - id: msin
+ type: Directory?
+ inputBinding:
+ position: 0
+ prefix: msin=
+ separate: false
+ doc: Input Measurement Set
+ - id: msout_name
+ default: "."
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: msout=
+ separate: false
+ doc: Output Measurement Set
+ - id: autoweight
+ default: false
+ type: boolean?
+ inputBinding:
+ position: 0
+ prefix: 'msin.autoweight=True'
+ - id: baseline
+ default: ''
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: 'msin.baseline='
+ separate: false
+ - id: output_column
+ default: DATA
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: 'msout.datacolumn='
+ separate: false
+ - id: input_column
+ default: DATA
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: 'msin.datacolumn='
+ separate: false
+ - id: writefullresflag
+ type: boolean?
+ default: false
+ inputBinding:
+ prefix: msout.writefullresflag=True
+ - id: overwrite
+ type: boolean?
+ default: false
+ inputBinding:
+ prefix: msout.overwrite=True
+ - id: storagemanager
+ type: string?
+ default: ""
+ inputBinding:
+ prefix: msout.storagemanager=
+ separate: false
+ - id: databitrate
+ type: int?
+ default: 0
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
+ - id: skymodel
+ type: File
+ inputBinding:
+ position: 0
+ prefix: demix.skymodel=
+ separate: false
+outputs:
+ - id: msout
+ doc: Output Measurement Set
+ type: Directory
+ outputBinding:
+ glob: '$(inputs.msout_name=="." ? inputs.msin.basename : inputs.msout_name)'
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'DPPP*.log'
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor3-cwl
+stdout: DPPP.log
+stderr: DPPP_err.log
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
diff --git a/steps/dppp_prep_target.cwl b/steps/dppp_prep_target.cwl
new file mode 100755
index 00000000..fa9060db
--- /dev/null
+++ b/steps/dppp_prep_target.cwl
@@ -0,0 +1,141 @@
+class: CommandLineTool
+cwlVersion: v1.1
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: dppp
+baseCommand:
+ - DP3
+inputs:
+ - id: parset
+ type: File?
+ inputBinding:
+ position: -1
+ - id: msin
+ type: Directory?
+ inputBinding:
+ position: 0
+ prefix: msin=
+ separate: false
+ doc: Input Measurement Set
+ - id: solutions
+ type: File?
+ doc: Input Solution Set
+ - id: msout_name
+ default: "."
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: msout=
+ separate: false
+ doc: Output Measurement Set
+ - id: autoweight
+ default: false
+ type: boolean?
+ inputBinding:
+ position: 0
+ prefix: 'msin.autoweight=True'
+ - id: baseline
+ default: ''
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: 'msin.baseline='
+ separate: false
+ - id: output_column
+ default: DATA
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: 'msout.datacolumn='
+ separate: false
+ - id: input_column
+ default: DATA
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: 'msin.datacolumn='
+ separate: false
+ - id: writefullresflag
+ type: boolean?
+ default: false
+ inputBinding:
+ prefix: msout.writefullresflag=True
+ - id: overwrite
+ type: boolean?
+ default: false
+ inputBinding:
+ prefix: msout.overwrite=True
+ - id: storagemanager
+ type: string?
+ default: ""
+ inputBinding:
+ prefix: msout.storagemanager=
+ separate: false
+ - id: databitrate
+ type: int?
+ default: 0
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
+ - id: apply_tec_correction
+ type: boolean?
+ default: false
+ inputBinding:
+ position: 0
+ prefix: 'applytec.parmdb='
+ separate: false
+ valueFrom: $(inputs.solutions.path)
+ - id: apply_rm_correction
+ type: boolean?
+ default: true
+ inputBinding:
+ position: 0
+ prefix: 'applyRM.parmdb='
+ separate: false
+ valueFrom: $(inputs.solutions.path)
+ - id: apply_phase_correction
+ type: boolean?
+ default: false
+ inputBinding:
+ position: 0
+ prefix: 'applyphase.parmdb='
+ separate: false
+ valueFrom: $(inputs.solutions.path)
+ - id: apply_clock_correction
+ type: boolean?
+ default: true
+ inputBinding:
+ position: 0
+ prefix: 'applyclock.parmdb='
+ separate: false
+ valueFrom: $(inputs.solutions.path)
+ - id: skymodel
+ type: File
+ inputBinding:
+ position: 0
+ prefix: demix.skymodel=
+ separate: false
+arguments:
+ - applyPA.parmdb=$(inputs.solutions.path)
+ - applybandpass.parmdb=$(inputs.solutions.path)
+outputs:
+ - id: msout
+ doc: Output Measurement Set
+ type: Directory
+ outputBinding:
+ glob: '$(inputs.msout_name=="." ? inputs.msin.basename : inputs.msout_name)'
+ - id: logfile
+ type: File[]
+ outputBinding:
+ glob: 'DPPP*.log'
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor3-cwl
+stdout: DPPP.log
+stderr: DPPP_err.log
+requirements:
+ - class: InlineJavascriptRequirement
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
diff --git a/steps/filter_ms_group.cwl b/steps/filter_ms_group.cwl
index e09eec16..2d1f5692 100644
--- a/steps/filter_ms_group.cwl
+++ b/steps/filter_ms_group.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: filter_ms_group
baseCommand:
- python3
@@ -73,6 +73,6 @@ hints:
listing:
- entry: $(inputs.measurement_sets)
writable: true
-
+
stdout: filter_ms_by_group.log
stderr: filter_ms_by_group_err.log
\ No newline at end of file
diff --git a/steps/findRefAnt.cwl b/steps/findRefAnt.cwl
index d4544091..77c842ea 100644
--- a/steps/findRefAnt.cwl
+++ b/steps/findRefAnt.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: findRefAnt
@@ -37,7 +37,7 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).flagged_fraction_dict)
- id: logfile
- type: File?
+ type: File
outputBinding:
glob: findRefAnt.log
diff --git a/steps/findRefAnt_join.cwl b/steps/findRefAnt_join.cwl
index e8ffabc8..c5916019 100644
--- a/steps/findRefAnt_join.cwl
+++ b/steps/findRefAnt_join.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: findRefAnt_join
@@ -30,11 +30,11 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).refant)
- id: flagged_fraction_antenna
- type: File?
+ type: File
outputBinding:
glob: 'flagged_fraction_antenna.json'
- id: logfile
- type: File?
+ type: File
outputBinding:
glob: findRefAnt.log
diff --git a/steps/find_skymodel_cal.cwl b/steps/find_skymodel_cal.cwl
index 7ee4e7ef..89b5997a 100644
--- a/steps/find_skymodel_cal.cwl
+++ b/steps/find_skymodel_cal.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: find_skymodel_cal_py
@@ -43,7 +43,7 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).skymodel_name)
- id: logfile
- type: File?
+ type: File
outputBinding:
glob: find_skymodel_cal.log
diff --git a/steps/find_skymodel_target.cwl b/steps/find_skymodel_target.cwl
index fcc32d18..b9c22a2f 100644
--- a/steps/find_skymodel_target.cwl
+++ b/steps/find_skymodel_target.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: find_skymodel_target_py
@@ -61,7 +61,7 @@ outputs:
outputBinding:
glob: target.skymodel
- id: logfile
- type: File?
+ type: File
outputBinding:
glob: find_skymodel_target.log
@@ -69,6 +69,7 @@ requirements:
- class: InlineJavascriptRequirement
hints:
- DockerRequirement:
+ - class: DockerRequirement
dockerPull: lofareosc/prefactor3-cwl
+
stdout: find_skymodel_target.log
\ No newline at end of file
diff --git a/steps/get_targetname.cwl b/steps/get_targetname.cwl
index 0bfa0572..491bf3fe 100644
--- a/steps/get_targetname.cwl
+++ b/steps/get_targetname.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
diff --git a/steps/h5parm_pointingname.cwl b/steps/h5parm_pointingname.cwl
index e1a99a38..06c90242 100644
--- a/steps/h5parm_pointingname.cwl
+++ b/steps/h5parm_pointingname.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
diff --git a/steps/h5parmcat.cwl b/steps/h5parmcat.cwl
index fdf076b5..36b62037 100644
--- a/steps/h5parmcat.cwl
+++ b/steps/h5parmcat.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
diff --git a/steps/identify_bad_antennas.cwl b/steps/identify_bad_antennas.cwl
index 1a2409ab..1f7b6630 100644
--- a/steps/identify_bad_antennas.cwl
+++ b/steps/identify_bad_antennas.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: identify_bad_antennas
@@ -38,7 +38,7 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).flaggedants)
- id: logfile
- type: File?
+ type: File
outputBinding:
glob: identifyBadAntennas.log
diff --git a/steps/identify_bad_antennas_join.cwl b/steps/identify_bad_antennas_join.cwl
index 8d2abd59..52042229 100644
--- a/steps/identify_bad_antennas_join.cwl
+++ b/steps/identify_bad_antennas_join.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: identify_bad_antennas_join
@@ -47,7 +47,7 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).filter)
- id: logfile
- type: File?
+ type: File
outputBinding:
glob: identifyBadAntennas.log
diff --git a/steps/merge_array.cwl b/steps/merge_array.cwl
index 7d8fef0a..14fcd046 100644
--- a/steps/merge_array.cwl
+++ b/steps/merge_array.cwl
@@ -2,7 +2,7 @@ id: merge_array
label: merge_array
class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
inputs:
- id: input
type:
diff --git a/steps/merge_array_files.cwl b/steps/merge_array_files.cwl
index c4c5c612..2ad56843 100644
--- a/steps/merge_array_files.cwl
+++ b/steps/merge_array_files.cwl
@@ -2,7 +2,7 @@ id: merge_array_files
label: merge_array_files
class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
inputs:
- id: input
type:
diff --git a/steps/plot_Ateamclipper.cwl b/steps/plot_Ateamclipper.cwl
index c9e19821..188972ed 100644
--- a/steps/plot_Ateamclipper.cwl
+++ b/steps/plot_Ateamclipper.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: plot_Ateamclipper
diff --git a/steps/plot_unflagged.cwl b/steps/plot_unflagged.cwl
index 48047a01..015d6ba7 100644
--- a/steps/plot_unflagged.cwl
+++ b/steps/plot_unflagged.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: plot_unflagged
@@ -38,7 +38,7 @@ outputs:
outputBinding:
glob: 'unflagged_fraction.png'
- id: logfile
- type: File[]?
+ type: File[]
outputBinding:
glob: 'plot_unflagged_fraction*.log'
diff --git a/steps/read_surl_list.cwl b/steps/read_surl_list.cwl
index b1527d08..43c7a42c 100644
--- a/steps/read_surl_list.cwl
+++ b/steps/read_surl_list.cwl
@@ -1,5 +1,5 @@
class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: read_surl_file
inputs:
- id: surl_list
diff --git a/steps/selectfirstdirectory.cwl b/steps/selectfirstdirectory.cwl
index c4ecb018..3175f9d6 100644
--- a/steps/selectfirstdirectory.cwl
+++ b/steps/selectfirstdirectory.cwl
@@ -2,7 +2,7 @@ id: selectfirstdirectory
label: selectfirstdirectory
class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
inputs:
- id: input
type: Directory[]
@@ -22,4 +22,3 @@ expression: |
${
return {'output': inputs.input[0]}
}
-
diff --git a/steps/selectfirstfile.cwl b/steps/selectfirstfile.cwl
index b928a3ff..d2a668e7 100644
--- a/steps/selectfirstfile.cwl
+++ b/steps/selectfirstfile.cwl
@@ -1,5 +1,5 @@
class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
id: select_first_file
inputs:
- id: inputs
diff --git a/steps/separate_results_directory.cwl b/steps/separate_results_directory.cwl
index a5e1389e..7bbb37f4 100644
--- a/steps/separate_results_directory.cwl
+++ b/steps/separate_results_directory.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: separate_results_directory
diff --git a/steps/sort_times_into_freqGroups.cwl b/steps/sort_times_into_freqGroups.cwl
index 3c3c14f8..4bf3c815 100644
--- a/steps/sort_times_into_freqGroups.cwl
+++ b/steps/sort_times_into_freqGroups.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: sort_times_into_freqGroups
@@ -89,7 +89,7 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).total_bandwidth)
- id: logfile
- type: File?
+ type: File
outputBinding:
glob: sort_times_into_freqGroups.log
@@ -99,4 +99,5 @@ requirements:
hints:
- class: DockerRequirement
dockerPull: lofareosc/prefactor3-cwl
-stdout: sort_times_into_freqGroups.log
\ No newline at end of file
+stdout: sort_times_into_freqGroups.log
+stderr: sort_times_into_freqGroups_err.log
\ No newline at end of file
diff --git a/steps/stage.cwl b/steps/stage.cwl
index 0cc4266a..7520bfdc 100644
--- a/steps/stage.cwl
+++ b/steps/stage.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: stage
diff --git a/steps/structure_function.cwl b/steps/structure_function.cwl
index bc138367..756129e7 100644
--- a/steps/structure_function.cwl
+++ b/steps/structure_function.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
diff --git a/steps/summary.cwl b/steps/summary.cwl
index 809299e1..bc3075cc 100644
--- a/steps/summary.cwl
+++ b/steps/summary.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
diff --git a/steps/surl_copy.cwl b/steps/surl_copy.cwl
index 08bd4527..15e45420 100644
--- a/steps/surl_copy.cwl
+++ b/steps/surl_copy.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: surl_copy
diff --git a/steps/transfer_solutions.cwl b/steps/transfer_solutions.cwl
index d58d3145..1296467d 100644
--- a/steps/transfer_solutions.cwl
+++ b/steps/transfer_solutions.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: transfer_solutions
diff --git a/steps/untar.cwl b/steps/untar.cwl
index 55d02a9d..0ca0dcf0 100644
--- a/steps/untar.cwl
+++ b/steps/untar.cwl
@@ -1,7 +1,7 @@
id: untar
label: untar
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
inputs:
- id: tar_file
type: File
diff --git a/steps/uvplot.cwl b/steps/uvplot.cwl
index 34a2a2aa..05f7fdda 100644
--- a/steps/uvplot.cwl
+++ b/steps/uvplot.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
diff --git a/subworkflow/apply_calibrate_bp.cwl b/subworkflow/apply_calibrate_bp.cwl
index de5863ce..e0e70ea9 100644
--- a/subworkflow/apply_calibrate_bp.cwl
+++ b/subworkflow/apply_calibrate_bp.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: apply_calibrate
label: apply_calibrate
$namespaces:
@@ -10,15 +10,18 @@ inputs:
'sbg:x': -1000
'sbg:y': -200
- id: do_smooth
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': -100
- id: flagunconverged
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': 100
- id: propagatesolutions
- type: boolean
+ type: boolean?
+ default: true
'sbg:x': -1000
'sbg:y': 200
- id: input_h5parm
diff --git a/subworkflow/apply_calibrate_fr.cwl b/subworkflow/apply_calibrate_fr.cwl
index 3c20638a..1350e1c9 100644
--- a/subworkflow/apply_calibrate_fr.cwl
+++ b/subworkflow/apply_calibrate_fr.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: apply_calibrate
label: apply_calibrate
$namespaces:
@@ -10,15 +10,18 @@ inputs:
'sbg:x': -1000
'sbg:y': -200
- id: do_smooth
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': -100
- id: flagunconverged
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': 100
- id: propagatesolutions
- type: boolean
+ type: boolean?
+ default: true
'sbg:x': -1000
'sbg:y': 200
- id: input_h5parm
diff --git a/subworkflow/apply_calibrate_pa.cwl b/subworkflow/apply_calibrate_pa.cwl
index c8f1ea5c..6fb98eb1 100644
--- a/subworkflow/apply_calibrate_pa.cwl
+++ b/subworkflow/apply_calibrate_pa.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: apply_calibrate
label: apply_calibrate
$namespaces:
@@ -10,15 +10,18 @@ inputs:
'sbg:x': -1000
'sbg:y': -200
- id: do_smooth
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': -100
- id: flagunconverged
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': 100
- id: propagatesolutions
- type: boolean
+ type: boolean?
+ default: true
'sbg:x': -1000
'sbg:y': 200
- id: input_h5parm
diff --git a/subworkflow/apply_calibration.cwl b/subworkflow/apply_calibration.cwl
index 7f6af5ac..f5ff47d8 100644
--- a/subworkflow/apply_calibration.cwl
+++ b/subworkflow/apply_calibration.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: apply_calibration
label: apply_calibration
$namespaces:
diff --git a/subworkflow/bandpass.cwl b/subworkflow/bandpass.cwl
index 63f7dc63..1d0f2bd0 100644
--- a/subworkflow/bandpass.cwl
+++ b/subworkflow/bandpass.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_bandpass
label: losoto_bandpass
$namespaces:
@@ -7,10 +7,12 @@ $namespaces:
inputs:
- id: ampRange
type: 'float[]?'
+ default: [0, 0]
'sbg:x': 397.4866943359375
'sbg:y': 73.48989868164062
- id: skipInternational
type: boolean?
+ default: false
'sbg:x': 401.4047546386719
'sbg:y': -185.20863342285156
- id: input_h5parm
@@ -19,14 +21,17 @@ inputs:
'sbg:y': -51.39104080200195
- id: max2interpolate
type: int?
+ default: 30
'sbg:x': 398.02581787109375
'sbg:y': -311.48223876953125
- id: bandpass_freqresolution
- type: string
+ type: string?
+ default: '195.3125kHz'
'sbg:x': 404.9237365722656
'sbg:y': -440.521484375
- id: avg_freqresolution
type: string?
+ default: '48.82kHz'
'sbg:x': 401.60693359375
'sbg:y': 198.58273315429688
outputs:
diff --git a/subworkflow/calib_cal.cwl b/subworkflow/calib_cal.cwl
index 1fceb82d..d2c09a9f 100644
--- a/subworkflow/calib_cal.cwl
+++ b/subworkflow/calib_cal.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: calibrate_calibrator
label: calibrate_calibrator
$namespaces:
@@ -11,6 +11,7 @@ inputs:
'sbg:y': -100
- id: do_smooth
type: boolean
+ default: false
'sbg:x': -1000
'sbg:y': 0
- id: sourcedb
diff --git a/subworkflow/calib_targ.cwl b/subworkflow/calib_targ.cwl
index 5ff661bb..b09da67e 100644
--- a/subworkflow/calib_targ.cwl
+++ b/subworkflow/calib_targ.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: calibrate_target
label: calibrate_target
$namespaces:
@@ -14,11 +14,13 @@ inputs:
'sbg:x': -1000
'sbg:y': -100
- id: do_smooth
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': 0
- id: propagatesolutions
- type: boolean
+ type: boolean?
+ default: true
'sbg:x': -1000
'sbg:y': 100
outputs:
diff --git a/subworkflow/clocktec.cwl b/subworkflow/clocktec.cwl
index 66c85694..6dedf0a6 100644
--- a/subworkflow/clocktec.cwl
+++ b/subworkflow/clocktec.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_ion
label: losoto_ion
$namespaces:
@@ -11,18 +11,22 @@ inputs:
'sbg:y': -400
- id: fit3rdorder
type: boolean?
+ default: false
'sbg:x': -700
'sbg:y': -200
- id: refAnt
type: string?
+ default: 'CS001HBA0'
'sbg:x': -700
'sbg:y': 0
- id: maxStddev
type: float?
+ default: -1.0
'sbg:x': -700
'sbg:y': 200
- id: clock_smooth
type: boolean?
+ default: true
'sbg:x': -700
'sbg:y': 400
outputs:
diff --git a/subworkflow/concat.cwl b/subworkflow/concat.cwl
index d2224d34..a7a3eb0c 100644
--- a/subworkflow/concat.cwl
+++ b/subworkflow/concat.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: concat
label: concat
$namespaces:
@@ -18,19 +18,23 @@ inputs:
'sbg:x': -1000
'sbg:y': -100
- id: filter_baselines
- type: string
+ type: string?
+ default: '*&'
'sbg:x': -1000
'sbg:y': 0
- id: avg_timeresolution_concat
- type: int
+ type: int?
+ default: 8
'sbg:x': -1000
'sbg:y': 100
- id: avg_freqresolution_concat
- type: string
+ type: string?
+ default: '97.64kHz'
'sbg:x': -1000
'sbg:y': 200
- id: min_unflagged_fraction
- type: float
+ type: float?
+ default: 0.5
'sbg:x': -1000
'sbg:y': 300
outputs:
@@ -115,4 +119,4 @@ steps:
'sbg:x': 600
'sbg:y': 200
-requirements: []
+requirements: []
\ No newline at end of file
diff --git a/subworkflow/faraday_rotation.cwl b/subworkflow/faraday_rotation.cwl
index 7afd26b6..350378d4 100644
--- a/subworkflow/faraday_rotation.cwl
+++ b/subworkflow/faraday_rotation.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: faraday_rotation
label: faraday_rotation
$namespaces:
@@ -8,6 +8,7 @@ $namespaces:
inputs:
- id: refAnt
type: string?
+ default: 'CS001HBA0'
'sbg:x': -451.3746643066406
'sbg:y': -493.92510986328125
- id: input_h5parm
diff --git a/subworkflow/ionosphere.cwl b/subworkflow/ionosphere.cwl
index 4d8ccac1..8b1b755a 100644
--- a/subworkflow/ionosphere.cwl
+++ b/subworkflow/ionosphere.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: ionosphere
label: ionosphere
$namespaces:
@@ -11,14 +11,17 @@ inputs:
'sbg:y': -21.5
- id: propagate_solutions
type: boolean
+ default: true
'sbg:x': -482.39886474609375
'sbg:y': -260.5
- id: flagunconverged
type: boolean
+ default: false
'sbg:x': -559.3988647460938
'sbg:y': 118.5
- id: do_smooth
type: boolean
+ default: false
'sbg:x': -420.39886474609375
'sbg:y': 229.5
outputs:
diff --git a/subworkflow/losoto_bandpass.cwl b/subworkflow/losoto_bandpass.cwl
index 4b668f7b..b1771a09 100644
--- a/subworkflow/losoto_bandpass.cwl
+++ b/subworkflow/losoto_bandpass.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_bandpass
label: losoto_bandpass
$namespaces:
@@ -7,10 +7,12 @@ $namespaces:
inputs:
- id: ampRange
type: 'float[]?'
+ default: [0, 0]
'sbg:x': 730.283935546875
'sbg:y': 152.7667236328125
- id: skipInternational
type: string?
+ default: true
'sbg:x': 742.662841796875
'sbg:y': -221.30563354492188
- id: input_h5parm
@@ -19,6 +21,7 @@ inputs:
'sbg:y': -41.42390060424805
- id: max2interpolate
type: int?
+ default: 30
'sbg:x': 1227
'sbg:y': -278
- id: bandpass_freqresolution
@@ -27,6 +30,7 @@ inputs:
'sbg:y': -354
- id: avg_freqresolution
type: string?
+ default: '48.82kHz'
'sbg:x': 1286.2171630859375
'sbg:y': 127.25900268554688
outputs:
diff --git a/subworkflow/losoto_ion.cwl b/subworkflow/losoto_ion.cwl
index 3eec42be..408f9754 100644
--- a/subworkflow/losoto_ion.cwl
+++ b/subworkflow/losoto_ion.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: losoto_ion
label: losoto_ion
$namespaces:
@@ -11,14 +11,17 @@ inputs:
'sbg:y': -147.5
- id: fit3rdorder
type: boolean?
+ default: false
'sbg:x': 83.60113525390625
'sbg:y': 53.5
- id: refAnt
type: string?
+ default: 'CS001HBA0'
'sbg:x': 500.74346923828125
'sbg:y': -382.8847351074219
- id: maxStddev
type: float?
+ default: -1.0
'sbg:x': 374.1950988769531
'sbg:y': -308.9609069824219
outputs:
diff --git a/subworkflow/ndppp_prep_cal.cwl b/subworkflow/ndppp_prep_cal.cwl
index 6bcdf446..8f46bd8d 100644
--- a/subworkflow/ndppp_prep_cal.cwl
+++ b/subworkflow/ndppp_prep_cal.cwl
@@ -1,310 +1,190 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: ndppp_prep_cal
label: ndppp_prep_cal
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: baselines_to_flag
- type: 'string[]'
- 'sbg:x': 732.2234497070312
- 'sbg:y': 79.11939239501953
+ type: 'string[]?'
+ default: []
+ 'sbg:x': -500
+ 'sbg:y': -800
- id: elevation_to_flag
- type: string
- 'sbg:x': 815.8416137695312
- 'sbg:y': -281.40777587890625
+ type: string?
+ default: '0deg..15deg'
+ 'sbg:x': -500
+ 'sbg:y': -700
- id: min_amplitude_to_flag
- type: float
- 'sbg:x': 964.3058471679688
- 'sbg:y': 191.110595703125
+ type: float?
+ default: 1e-30
+ 'sbg:x': -500
+ 'sbg:y': -600
- id: memoryperc
- type: int
- 'sbg:x': 136.78256225585938
- 'sbg:y': -341.9549560546875
+ type: int?
+ default: 20
+ 'sbg:x': -500
+ 'sbg:y': -500
- id: raw_data
- type: boolean
- 'sbg:x': 444.4574279785156
- 'sbg:y': -343.6958312988281
+ type: boolean?
+ default: false
+ 'sbg:x': -500
+ 'sbg:y': -400
- id: demix
- type: boolean
- 'sbg:x': 1736.6195068359375
- 'sbg:y': -298.45196533203125
+ type: boolean?
+ default: false
+ 'sbg:x': -500
+ 'sbg:y': -300
- id: msin
- type: Directory?
- 'sbg:x': 2306.83056640625
- 'sbg:y': 318.2810363769531
+ type: Directory
+ 'sbg:x': -500
+ 'sbg:y': -200
- id: msin_baseline
type: string?
- 'sbg:x': 2273.798583984375
- 'sbg:y': 182.7539825439453
+ default: '*&'
+ 'sbg:x': -500
+ 'sbg:y': -100
- id: skymodel
type: File
- 'sbg:x': 1335.2567138671875
- 'sbg:y': 148.68453979492188
+ 'sbg:x': -500
+ 'sbg:y': 0
- id: timeresolution
- type: float
- 'sbg:x': 2021.81787109375
- 'sbg:y': -352.4759216308594
+ type: int?
+ default: 4
+ 'sbg:x': -500
+ 'sbg:y': 100
- id: freqresolution
- type: string
- 'sbg:x': 1999.5889892578125
- 'sbg:y': 170.7563934326172
+ type: string?
+ default: '48.82kHz'
+ 'sbg:x': -500
+ 'sbg:y': 200
- id: demix_timestep
- type: int
- 'sbg:x': 1371.962646484375
- 'sbg:y': 307.4278259277344
+ type: int?
+ default: 10
+ 'sbg:x': -500
+ 'sbg:y': 300
- id: demix_freqstep
- type: int
- 'sbg:x': 1465.0855712890625
- 'sbg:y': 450.8930358886719
+ type: int?
+ default: 16
+ 'sbg:x': -500
+ 'sbg:y': 400
- id: demix_baseline
- type: string
- 'sbg:x': 1585.496826171875
- 'sbg:y': 588.0062866210938
+ type: string?
+ default: '*&'
+ 'sbg:x': -500
+ 'sbg:y': 500
- id: target_source
- type: string
- 'sbg:x': 1439.47314453125
- 'sbg:y': -325.6144104003906
+ type: string?
+ default: ''
+ 'sbg:x': -500
+ 'sbg:y': 600
- id: ntimechunk
- type: int
- 'sbg:x': 1149.4033203125
- 'sbg:y': 349.2409362792969
+ type: int?
+ default: 16
+ 'sbg:x': -500
+ 'sbg:y': 700
- id: subtract_sources
type: 'string[]?'
- 'sbg:x': 1257.9327392578125
- 'sbg:y': -290.095703125
+ default: []
+ 'sbg:x': -500
+ 'sbg:y': 800
outputs:
- id: msout
outputSource:
- - dppp/msout
+ - dp3_execute/msout
type: Directory
- 'sbg:x': 2856.537841796875
- 'sbg:y': 53.67763900756836
+ 'sbg:x': 1000
+ 'sbg:y': -100
- id: logfile
outputSource:
- concat_logfiles_dppp/output
type: File
- 'sbg:x': 2857.9423828125
- 'sbg:y': 253.50680541992188
- - id: parset
- outputSource:
- - parsetgenerator/parset
- type: File
- 'sbg:x': 2598.6884765625
- 'sbg:y': -303.1161804199219
+ 'sbg:x': 1000
+ 'sbg:y': 0
steps:
- - id: flagbaseline
- in:
- - id: steps
- source:
- - process_raw_data_select/selected_steps
- - id: step_name
- default: flagbaseline
- - id: baseline
- source:
- - baselines_to_flag
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
- 'sbg:x': 955.2450561523438
- 'sbg:y': -75.71149444580078
- - id: flagelev
- in:
- - id: steps
- source:
- - flagbaseline/augmented_steps
- - id: step_name
- default: flagelev
- - id: elevation
- source: elevation_to_flag
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
- 'sbg:x': 1187.4771728515625
- 'sbg:y': -83
- - id: process_raw_data_select
+ - id: define_parset
in:
- - id: select_a
+ - id: raw_data
source: raw_data
- - id: a_steps
- source:
- - aoflag/augmented_steps
- - id: b_steps
- default: []
- out:
- - id: selected_steps
- run: ../lofar-cwl/steps/DP3.Selector.cwl
- label: Selector
- 'sbg:x': 621.4892578125
- 'sbg:y': -71.31844329833984
- - id: flagamp
- in:
- - id: steps
- source:
- - flagelev/augmented_steps
- - id: step_name
- default: flagamp
- - id: amplmin
- source: min_amplitude_to_flag
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
- 'sbg:x': 1385.993408203125
- 'sbg:y': -42.28850555419922
- - id: flagedge
- in:
- - id: steps
- default: []
- - id: step_name
- default: flagedge
- - id: chan
- default: '[0..nchan/32-1,31*nchan/32..nchan-1]'
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
- 'sbg:x': 122.25408935546875
- 'sbg:y': -54.06163024902344
- - id: aoflag
- in:
- - id: steps
- source:
- - flagedge/augmented_steps
- - id: step_name
- default: aoflag
+ - id: demix
+ source: demix
+ - id: filter_baselines
+ source: msin_baseline
- id: memoryperc
source: memoryperc
- - id: keepstatistics
- default: false
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl
- 'sbg:x': 369.9876708984375
- 'sbg:y': -38.086280822753906
- - id: demix_select
- in:
- - id: select_a
- source: demix
- - id: a_steps
+ - id: baselines_to_flag
source:
- - demixstepgenerator/augmented_steps
- - id: b_steps
- source:
- - flagamp/augmented_steps
- out:
- - id: selected_steps
- run: ../lofar-cwl/steps/DP3.Selector.cwl
- label: demix?
- 'sbg:x': 1974.7406005859375
- 'sbg:y': -32.03063201904297
- - id: demixstepgenerator
- in:
- - id: steps
- source:
- - flagamp/augmented_steps
- - id: step_name
- default: demixer
- - id: baseline
+ - baselines_to_flag
+ - id: elevation_to_flag
+ source: elevation_to_flag
+ - id: min_amplitude_to_flag
+ source: min_amplitude_to_flag
+ - id: timeresolution
+ source: timeresolution
+ - id: freqresolution
+ source: freqresolution
+ - id: process_baselines_cal
source: demix_baseline
- - id: demixtimestep
+ - id: demix_timestep
source: demix_timestep
- - id: demixfreqstep
+ - id: demix_freqstep
source: demix_freqstep
- - id: ntimechunk
- source: ntimechunk
- - id: skymodel
- source: skymodel
- - id: subtractsources
- source:
- - subtract_sources
- - id: targetsource
+ - id: target_source
source: target_source
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.DemixerStepGenerator.cwl
- 'sbg:x': 1676.6593017578125
- 'sbg:y': 90.7158203125
- - id: parsetgenerator
- in:
- - id: steps
+ - id: subtract_sources
source:
- - average_step_generator/augmented_steps
+ - subtract_sources
+ - id: ntimechunk
+ source: ntimechunk
out:
- - id: parset
- - id: input_files
- - id: input_directories
- - id: output_file_names
- - id: output_directory_names
- run: ../lofar-cwl/steps/DP3.ParsetGenerator.cwl
- 'sbg:x': 2340.85400390625
- 'sbg:y': -79.32791900634766
- - id: dppp
+ - id: output
+ run: ../steps/dppp_make_parset_cal.cwl
+ label: make_parset
+ 'sbg:x': 0
+ 'sbg:y': 0
+ - id: dp3_execute
in:
- id: parset
- source: parsetgenerator/parset
+ source: define_parset/output
- id: msin
source: msin
- id: msout_name
source: msin
valueFrom: $("out_"+self.basename)
- - id: secondary_files
- source:
- - parsetgenerator/input_files
- - id: secondary_directories
- source:
- - parsetgenerator/input_directories
- - id: output_file_names
- source: parsetgenerator/output_file_names
- - id: output_directory_names
- source: parsetgenerator/output_directory_names
- id: autoweight
source: raw_data
- id: baseline
source: msin_baseline
- - id: writefullresflag
- default: false
+ - id: output_column
+ default: DATA
+ - id: input_column
+ default: DATA
- id: storagemanager
default: Dysco
- id: databitrate
default: 0
+ - id: skymodel
+ source: skymodel
out:
- id: msout
- - id: secondary_output_files
- - id: secondary_output_directories
- id: logfile
- run: ../lofar-cwl/steps/DPPP.cwl
- 'sbg:x': 2669.29345703125
- 'sbg:y': -42.129730224609375
- - id: average_step_generator
- in:
- - id: steps
- source:
- - demix_select/selected_steps
- - id: step_name
- default: averager
- - id: timeresolution
- source: timeresolution
- - id: freqresolution
- source: freqresolution
- - id: minpoints
- default: 1
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
- 'sbg:x': 2158.297119140625
- 'sbg:y': -55.93873977661133
+ run: ../steps/dppp_prep_cal.cwl
+ label: DP3.Execute
+ 'sbg:x': 500
+ 'sbg:y': 0
- id: concat_logfiles_dppp
in:
- id: file_list
source:
- - dppp/logfile
+ - dp3_execute/logfile
- id: file_prefix
default: dppp
out:
- id: output
run: ../steps/concatenate_files.cwl
label: concat_logfiles_dppp
- 'sbg:x': 2759.2265625
- 'sbg:y': 140.91714477539062
+ 'sbg:x': 700
+ 'sbg:y': -200
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
diff --git a/subworkflow/ndppp_prep_targ.cwl b/subworkflow/ndppp_prep_targ.cwl
index f40d3ad3..e6821068 100644
--- a/subworkflow/ndppp_prep_targ.cwl
+++ b/subworkflow/ndppp_prep_targ.cwl
@@ -1,106 +1,127 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: ndppp_prep_targ
label: ndppp_prep_targ
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: baselines_to_flag
- type: 'string[]'
- 'sbg:x': 732.2234497070312
- 'sbg:y': 79.11939239501953
+ type: 'string[]?'
+ default: []
+ 'sbg:x': -500
+ 'sbg:y': -1000
- id: elevation_to_flag
- type: string
- 'sbg:x': 815.8416137695312
- 'sbg:y': -281.40777587890625
+ type: string?
+ default: '0deg..15deg'
+ 'sbg:x': -500
+ 'sbg:y': -900
- id: min_amplitude_to_flag
- type: float
- 'sbg:x': 964.3058471679688
- 'sbg:y': 191.110595703125
+ type: float?
+ default: 1e-30
+ 'sbg:x': -500
+ 'sbg:y': -800
- id: memoryperc
- type: int
- 'sbg:x': 136.78256225585938
- 'sbg:y': -341.9549560546875
+ type: int?
+ default: 20
+ 'sbg:x': -500
+ 'sbg:y': -700
- id: raw_data
- type: boolean
- 'sbg:x': 464.3541259765625
- 'sbg:y': -200.52120971679688
+ type: boolean?
+ default: false
+ 'sbg:x': -500
+ 'sbg:y': -600
- id: demix
- type: boolean
- 'sbg:x': 1647.1820068359375
- 'sbg:y': -314.6533508300781
+ type: boolean?
+ default: false
+ 'sbg:x': -500
+ 'sbg:y': -500
- id: msin
- type: Directory?
- 'sbg:x': 3819.599853515625
- 'sbg:y': 423.25006103515625
+ type: Directory
+ 'sbg:x': -500
+ 'sbg:y': -400
- id: skymodel
type: File
- 'sbg:x': 1335.2567138671875
- 'sbg:y': 148.68453979492188
+ 'sbg:x': -500
+ 'sbg:y': -300
- id: timeresolution
- type: float
- 'sbg:x': 3344.8515625
- 'sbg:y': -733.585693359375
+ type: int?
+ default: 4
+ 'sbg:x': -500
+ 'sbg:y': -200
- id: freqresolution
- type: string
- 'sbg:x': 3358.795654296875
- 'sbg:y': 298.08917236328125
+ type: string?
+ default: '48.82kHz'
+ 'sbg:x': -500
+ 'sbg:y': -100
- id: demix_timestep
- type: int
- 'sbg:x': 1371.962646484375
- 'sbg:y': 307.4278259277344
+ type: int?
+ default: 10
+ 'sbg:x': -500
+ 'sbg:y': 0
- id: demix_freqstep
- type: int
- 'sbg:x': 1465.0855712890625
- 'sbg:y': 450.8930358886719
+ type: int?
+ default: 16
+ 'sbg:x': -500
+ 'sbg:y': 100
- id: process_baselines_target
- type: string
- 'sbg:x': 1585.496826171875
- 'sbg:y': 588.0062866210938
+ type: string?
+ default: '[CR]S*&'
+ 'sbg:x': -500
+ 'sbg:y': 200
- id: target_source
- type: string
- 'sbg:x': 1439.47314453125
- 'sbg:y': -325.6144104003906
+ type: string?
+ default: ''
+ 'sbg:x': -500
+ 'sbg:y': 300
- id: ntimechunk
- type: int
- 'sbg:x': 1149.4033203125
- 'sbg:y': 349.2409362792969
+ type: int?
+ default: 16
+ 'sbg:x': -500
+ 'sbg:y': 400
- id: subtract_sources
type: 'string[]?'
- 'sbg:x': 1257.9327392578125
- 'sbg:y': -290.095703125
+ default: []
+ 'sbg:x': -500
+ 'sbg:y': 500
- id: parmdb
type: File
- 'sbg:x': 1930.5469970703125
- 'sbg:y': 298.99664306640625
+ 'sbg:x': -500
+ 'sbg:y': 600
- id: apply_tec_correction
- type: boolean
- 'sbg:x': 2310.848876953125
- 'sbg:y': 446.3658752441406
+ type: boolean?
+ default: false
+ 'sbg:x': -500
+ 'sbg:y': 700
- id: apply_rm_correction
- type: boolean
- 'sbg:x': 2461.30224609375
- 'sbg:y': 719.8994140625
+ type: boolean?
+ default: true
+ 'sbg:x': -500
+ 'sbg:y': 800
- id: apply_phase_correction
- type: boolean
- 'sbg:x': 2544.00341796875
- 'sbg:y': 844.8623657226562
+ type: boolean?
+ default: false
+ 'sbg:x': -500
+ 'sbg:y': 900
- id: apply_clock_correction
- type: boolean
- 'sbg:x': 2238.046630859375
- 'sbg:y': 327.0130920410156
+ type: boolean?
+ default: true
+ 'sbg:x': -500
+ 'sbg:y': 1000
- id: apply_beam_correction
- type: boolean
- 'sbg:x': 2391.738037109375
- 'sbg:y': 585.3051147460938
+ type: boolean?
+ default: true
+ 'sbg:x': -500
+ 'sbg:y': 1100
- id: filter_baselines
- type: string
- 'sbg:x': 1880
- 'sbg:y': -380
+ type: string?
+ default: ''
+ 'sbg:x': -500
+ 'sbg:y': 1200
- id: updateweights
- type: boolean
- 'sbg:x': 2234.90185546875
- 'sbg:y': -393.8929748535156
+ type: boolean?
+ default: true
+ 'sbg:x': -500
+ 'sbg:y': 1300
- id: clip_sources
type: 'string[]?'
default:
@@ -108,200 +129,98 @@ inputs:
- CygAGG
- CasA_4_patch
- TauAGG
- 'sbg:x': 4000
- 'sbg:y': -700
+ 'sbg:x': -500
+ 'sbg:y': 1400
outputs:
- id: prep_flags_out
outputSource:
- prep_flags/flagged_fraction_dict
- type: string?
- 'sbg:x': 5500
+ type: string
+ 'sbg:x': 2000
'sbg:y': 200
- id: prep_logfile
outputSource:
- concat_logfiles_dppp/output
- type: File?
- 'sbg:x': 5500
+ type: File
+ 'sbg:x': 2000
'sbg:y': 100
- id: predict_logfile
outputSource:
- concat_logfiles_predict/output
- type: File?
- 'sbg:x': 5500
+ type: File
+ 'sbg:x': 2000
'sbg:y': 0
- id: clipper_logfile
outputSource:
- concat_logfiles_clipper/output
- type: File?
- 'sbg:x': 5500
+ type: File
+ 'sbg:x': 2000
'sbg:y': -100
- id: msout
outputSource:
- Ateamclipper/msout
type: Directory
- 'sbg:x': 5502.318359375
- 'sbg:y': -279.49835205078125
+ 'sbg:x': 2000
+ 'sbg:y': -200
- id: clipper_output
outputSource:
- Ateamclipper/output
type: File
- 'sbg:x': 5502.318359375
- 'sbg:y': -500
- - id: parset
- outputSource:
- - dp3_execute/parset
- type: File
- 'sbg:x': 5427.662109375
- 'sbg:y': -765.5377197265625
+ 'sbg:x': 2000
+ 'sbg:y': -300
steps:
- - id: flagbaseline
- in:
- - id: steps
- source:
- - process_raw_data_select/selected_steps
- - id: step_name
- default: flagbaseline
- - id: baseline
- source:
- - baselines_to_flag
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
- 'sbg:x': 955.2450561523438
- 'sbg:y': -75.71149444580078
- - id: flagelev
- in:
- - id: steps
- source:
- - flagbaseline/augmented_steps
- - id: step_name
- default: flagelev
- - id: elevation
- source: elevation_to_flag
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
- 'sbg:x': 1187.4771728515625
- 'sbg:y': -83
- - id: process_raw_data_select
+ - id: define_parset
in:
- - id: select_a
+ - id: raw_data
source: raw_data
- - id: a_steps
- source:
- - aoflag/augmented_steps
- - id: b_steps
- default: []
- out:
- - id: selected_steps
- run: ../lofar-cwl/steps/DP3.Selector.cwl
- label: Selector
- 'sbg:x': 621.4892578125
- 'sbg:y': -71.31844329833984
- - id: flagamp
- in:
- - id: steps
- source:
- - flagelev/augmented_steps
- - id: step_name
- default: flagamp
- - id: amplmin
- source: min_amplitude_to_flag
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
- 'sbg:x': 1385.993408203125
- 'sbg:y': -42.28850555419922
- - id: flagedge
- in:
- - id: steps
- default: []
- - id: step_name
- default: flagedge
- - id: chan
- default: '[0..nchan/32-1,31*nchan/32..nchan-1]'
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
- 'sbg:x': 122.25408935546875
- 'sbg:y': -54.06163024902344
- - id: aoflag
- in:
- - id: steps
- source:
- - flagedge/augmented_steps
- - id: step_name
- default: aoflag
+ - id: demix
+ source: demix
+ - id: apply_tec_correction
+ source: apply_tec_correction
+ - id: apply_rm_correction
+ source: apply_rm_correction
+ - id: apply_phase_correction
+ source: apply_phase_correction
+ - id: apply_clock_correction
+ source: apply_clock_correction
+ - id: apply_beam_correction
+ source: apply_beam_correction
+ - id: filter_baselines
+ source: filter_baselines
- id: memoryperc
source: memoryperc
- - id: keepstatistics
- default: false
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl
- 'sbg:x': 369.9876708984375
- 'sbg:y': -38.086280822753906
- - id: demix_select
- in:
- - id: select_a
- source: demix
- - id: a_steps
- source:
- - demixstepgenerator/augmented_steps
- - id: b_steps
- source:
- - flagamp/augmented_steps
- out:
- - id: selected_steps
- run: ../lofar-cwl/steps/DP3.Selector.cwl
- label: demix?
- 'sbg:x': 1888.8828125
- 'sbg:y': -24.5985050201416
- - id: demixstepgenerator
- in:
- - id: steps
+ - id: baselines_to_flag
source:
- - flagamp/augmented_steps
- - id: step_name
- default: demixer
- - id: baseline
+ - baselines_to_flag
+ - id: elevation_to_flag
+ source: elevation_to_flag
+ - id: min_amplitude_to_flag
+ source: min_amplitude_to_flag
+ - id: updateweights
+ source: updateweights
+ - id: timeresolution
+ source: timeresolution
+ - id: freqresolution
+ source: freqresolution
+ - id: process_baselines_target
source: process_baselines_target
- - id: demixtimestep
+ - id: demix_timestep
source: demix_timestep
- - id: demixfreqstep
+ - id: demix_freqstep
source: demix_freqstep
- - id: ntimechunk
- source: ntimechunk
- - id: skymodel
- source: skymodel
- - id: subtractsources
- source:
- - subtract_sources
- - id: targetsource
+ - id: target_source
source: target_source
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.DemixerStepGenerator.cwl
- 'sbg:x': 1676.6593017578125
- 'sbg:y': 90.7158203125
- - id: average_step_generator
- in:
- - id: steps
+ - id: subtract_sources
source:
- - prep_target_applycal/selected_steps
- - id: step_name
- default: averager
- - id: minpoints
- default: 1
- - id: timeresolution
- source: timeresolution
- - id: freqresolution
- source: freqresolution
+ - subtract_sources
+ - id: ntimechunk
+ source: ntimechunk
out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
- 'sbg:x': 3743.862060546875
- 'sbg:y': -426.2447814941406
+ - id: output
+ run: ../steps/dppp_make_parset_target.cwl
+ label: make_parset
+ 'sbg:x': 0
+ 'sbg:y': 0
- id: concat_logfiles_dppp
in:
- id: file_list
@@ -313,8 +232,8 @@ steps:
- id: output
run: ../steps/concatenate_files.cwl
label: concat_logfiles_dppp
- 'sbg:x': 4543.36376953125
- 'sbg:y': -6.564670085906982
+ 'sbg:x': 1200
+ 'sbg:y': -500
- id: concat_logfiles_predict
in:
- id: file_list
@@ -326,8 +245,8 @@ steps:
- id: output
run: ../steps/concatenate_files.cwl
label: concat_logfiles_predict
- 'sbg:x': 4700
- 'sbg:y': -6.564670085906982
+ 'sbg:x': 1400
+ 'sbg:y': -500
- id: concat_logfiles_clipper
in:
- id: file_list
@@ -339,108 +258,40 @@ steps:
- id: output
run: ../steps/concatenate_files.cwl
label: concat_logfiles_clipper
- 'sbg:x': 4900
- 'sbg:y': -6.564670085906982
+ 'sbg:x': 1600
+ 'sbg:y': -500
- id: dp3_execute
in:
+ - id: parset
+ source: define_parset/output
+ - id: msin
+ source: msin
+ - id: solutions
+ source: parmdb
- id: msout_name
source: msin
valueFrom: $("out_"+self.basename)
- - id: msin
- source: msin
- - id: steps
- source:
- - average_step_generator/augmented_steps
- id: autoweight
- default: false
source: raw_data
+ - id: baseline
+ source: filter_baselines
+ - id: output_column
+ default: DATA
+ - id: input_column
+ default: DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ - id: skymodel
+ source: skymodel
out:
- - id: secondary_output_files
- - id: secondary_output_directories
- id: msout
- id: logfile
- - id: parset
- run: ../lofar-cwl/steps/DP3.Execute.cwl
+ run: ../steps/dppp_prep_target.cwl
label: DP3.Execute
- 'sbg:x': 4154.9287109375
- 'sbg:y': -344.5472106933594
- - id: filter
- in:
- - id: steps
- source:
- - demix_select/selected_steps
- - id: step_name
- default: filter
- - id: baseline
- source: filter_baselines
- - id: remove
- default: true
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.FilterStepGenerator.cwl
- 'sbg:x': 2049.48486328125
- 'sbg:y': -18.005611419677734
- - id: applyPA
- in:
- - id: steps
- source:
- - filter/augmented_steps
- - id: step_name
- default: apply_pa_1
- - id: parmdb
- source: parmdb
- - id: solset
- default: calibrator
- - id: correction
- default: polalign
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
- 'sbg:x': 2205.820068359375
- 'sbg:y': 7.381086349487305
- - id: applyBandpass
- in:
- - id: steps
- source:
- - applyPA/augmented_steps
- - id: step_name
- default: apply_bandpass_1
- - id: parmdb
- source: parmdb
- - id: solset
- default: calibrator
- - id: correction
- default: bandpass
- out:
- - id: augmented_steps
- run: ../lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
- 'sbg:x': 2420.382568359375
- 'sbg:y': -149.9799346923828
- - id: prep_target_applycal
- in:
- - id: steps
- source:
- - applyBandpass/augmented_steps
- - id: apply_clock_correction
- source: apply_clock_correction
- - id: apply_tec_correction
- source: apply_tec_correction
- - id: apply_rm_correction
- source: apply_rm_correction
- - id: apply_beam_correction
- source: apply_beam_correction
- - id: apply_phase_correction
- source: apply_phase_correction
- - id: parmdb
- source: parmdb
- - id: updateweights
- source: updateweights
- out:
- - id: selected_steps
- run: ./prep_target_applycal.cwl
- label: prep_target_applycal
- 'sbg:x': 2728.697998046875
- 'sbg:y': -18.151018142700195
+ 'sbg:x': 500
+ 'sbg:y': 0
- id: predict
in:
- id: msin
@@ -452,7 +303,8 @@ steps:
- id: sources_db
source: skymodel
- id: sources
- source: clip_sources
+ source:
+ - clip_sources
- id: usebeammodel
default: true
- id: onebeamperpatch
@@ -465,8 +317,8 @@ steps:
- id: msout
- id: logfile
run: ../lofar-cwl/steps/filter_predict.cwl
- 'sbg:x': 4500
- 'sbg:y': -344.5472106933594
+ 'sbg:x': 1000
+ 'sbg:y': 0
- id: prep_flags
in:
- id: msin
@@ -476,8 +328,8 @@ steps:
- id: logfile
run: ./../steps/findRefAnt.cwl
label: prep_flags
- 'sbg:x': 4500
- 'sbg:y': -600
+ 'sbg:x': 1500
+ 'sbg:y': 500
- id: Ateamclipper
in:
- id: msin
@@ -489,8 +341,8 @@ steps:
- id: output
run: ../lofar-cwl/steps/Ateamclipper.cwl
label: Ateamclipper
- 'sbg:x': 4700
- 'sbg:y': -344.5472106933594
+ 'sbg:x': 1300
+ 'sbg:y': 0
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
diff --git a/subworkflow/pol_align.cwl b/subworkflow/pol_align.cwl
index ee2d7dbd..b354b045 100644
--- a/subworkflow/pol_align.cwl
+++ b/subworkflow/pol_align.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: pol_align
label: PolAlign
$namespaces:
diff --git a/subworkflow/predict_calibrate.cwl b/subworkflow/predict_calibrate.cwl
index 4186dd11..b212217d 100644
--- a/subworkflow/predict_calibrate.cwl
+++ b/subworkflow/predict_calibrate.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: predict_calibrate
label: predict_calibrate
$namespaces:
@@ -10,7 +10,8 @@ inputs:
'sbg:x': -1000
'sbg:y': -200
- id: do_smooth
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': -100
- id: sourcedb
@@ -18,11 +19,13 @@ inputs:
'sbg:x': -1000
'sbg:y': 0
- id: flagunconverged
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': 100
- id: propagatesolutions
- type: boolean
+ type: boolean?
+ default: true
'sbg:x': -1000
'sbg:y': 200
outputs:
diff --git a/subworkflow/prep_target_applycal.cwl b/subworkflow/prep_target_applycal.cwl
index 04036992..ae613386 100644
--- a/subworkflow/prep_target_applycal.cwl
+++ b/subworkflow/prep_target_applycal.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: prep_target_applycal
label: prep_target_applycal
$namespaces:
diff --git a/subworkflow/smooth_calibrate.cwl b/subworkflow/smooth_calibrate.cwl
index 8995c3b0..bae17b55 100644
--- a/subworkflow/smooth_calibrate.cwl
+++ b/subworkflow/smooth_calibrate.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: smooth_calibrate
label: smooth_calibrate
$namespaces:
diff --git a/test_scatter/1st-tool.cwl b/test_scatter/1st-tool.cwl
index 4318c475..e1cea47d 100644
--- a/test_scatter/1st-tool.cwl
+++ b/test_scatter/1st-tool.cwl
@@ -1,6 +1,6 @@
#!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.1
class: CommandLineTool
baseCommand: echo
inputs:
diff --git a/test_scatter/cat.cwl b/test_scatter/cat.cwl
index 2ce25bce..ad364596 100644
--- a/test_scatter/cat.cwl
+++ b/test_scatter/cat.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: cat
diff --git a/test_scatter/scatter-workflow.cwl b/test_scatter/scatter-workflow.cwl
index 5ab2a692..366f9c5a 100644
--- a/test_scatter/scatter-workflow.cwl
+++ b/test_scatter/scatter-workflow.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
diff --git a/test_scatter/scattertest.cwl b/test_scatter/scattertest.cwl
index 3cf5b624..debd64a8 100644
--- a/test_scatter/scattertest.cwl
+++ b/test_scatter/scattertest.cwl
@@ -3,7 +3,7 @@ $namespaces:
id: scattertest
label: scattertest
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
inputs: []
outputs: []
steps: []
diff --git a/test_scatter/two_files.cwl b/test_scatter/two_files.cwl
index 1970c508..9234a4e8 100644
--- a/test_scatter/two_files.cwl
+++ b/test_scatter/two_files.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: two_files
label: two_files
$namespaces:
diff --git a/test_workflow/flag_average.cwl b/test_workflow/flag_average.cwl
index 921a3be5..0c9343ca 100644
--- a/test_workflow/flag_average.cwl
+++ b/test_workflow/flag_average.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: test
label: test
$namespaces:
diff --git a/test_workflow/two_steps.cwl b/test_workflow/two_steps.cwl
index 02f0143c..cc06d7ea 100644
--- a/test_workflow/two_steps.cwl
+++ b/test_workflow/two_steps.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: prefactor
$namespaces:
sbg: 'https://www.sevenbridges.com'
diff --git a/workflows/HBA_calibrator.cwl b/workflows/HBA_calibrator.cwl
index 906d905d..c305f321 100644
--- a/workflows/HBA_calibrator.cwl
+++ b/workflows/HBA_calibrator.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: HBA_calibrator
label: HBA_calibrator
$namespaces:
@@ -186,7 +186,7 @@ inputs:
'sbg:x': -1000
'sbg:y': 1600
- id: avg_timeresolution
- type: float?
+ type: int?
default: 4
'sbg:x': -1000
'sbg:y': 1700
@@ -374,5 +374,4 @@ steps:
'sbg:y': 0
requirements:
- class: SubworkflowFeatureRequirement
- - class: MultipleInputFeatureRequirement
-
+ - class: MultipleInputFeatureRequirement
\ No newline at end of file
diff --git a/workflows/HBA_target.cwl b/workflows/HBA_target.cwl
index d5d1399c..3c29be6e 100644
--- a/workflows/HBA_target.cwl
+++ b/workflows/HBA_target.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: HBA_target
label: HBA_target
$namespaces:
@@ -91,27 +91,27 @@ inputs:
'sbg:x': -1000
'sbg:y': -100
- id: apply_tec
- type: boolean
+ type: boolean?
default: false
'sbg:x': -1000
'sbg:y': 0
- id: apply_clock
- type: boolean
+ type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 100
- id: apply_phase
- type: boolean
+ type: boolean?
default: false
'sbg:x': -1000
'sbg:y': 200
- id: apply_RM
- type: boolean
+ type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 300
- id: apply_beam
- type: boolean
+ type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 400
@@ -219,7 +219,7 @@ inputs:
'sbg:x': -1000
'sbg:y': 2500
- id: proxy_port
- type: string?
+ type: int?
default: null
'sbg:x': -1000
'sbg:y': 2600
@@ -445,4 +445,4 @@ steps:
'sbg:y': 0
requirements:
- class: SubworkflowFeatureRequirement
- - class: MultipleInputFeatureRequirement
+ - class: MultipleInputFeatureRequirement
\ No newline at end of file
diff --git a/workflows/dowload_surl_and_create_input_file-json.cwl b/workflows/dowload_surl_and_create_input_file-json.cwl
index 328385f3..c3490d78 100644
--- a/workflows/dowload_surl_and_create_input_file-json.cwl
+++ b/workflows/dowload_surl_and_create_input_file-json.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: dowload_surl_and_create_input_file_json
label: dowload_surl_and_create_input_file.json
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index ded68950..13e75238 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/workflows/prefactor_calibrator.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: prefactor_calibrator
label: prefactor_calibrator
$namespaces:
@@ -186,7 +186,7 @@ inputs:
'sbg:x': -1000
'sbg:y': 1600
- id: avg_timeresolution
- type: float?
+ type: int?
default: 4
'sbg:x': -1000
'sbg:y': 1700
@@ -322,7 +322,6 @@ steps:
- id: check_Ateam_separation.png
- id: check_Ateam_separation.json
- id: msout
- - id: parset
- id: calibrator_name
run: ./prefactor_calibrator/prep.cwl
label: prep
@@ -442,8 +441,6 @@ steps:
- id: h5parm
source:
- fr/outh5parm
- - id: refant
- source: findRefAnt_join/refant
- id: inh5parm_logfile
source:
- fr/outh5parm_logfile
diff --git a/workflows/prefactor_calibrator/bp.cwl b/workflows/prefactor_calibrator/bp.cwl
index 1a43352a..9a4328a3 100644
--- a/workflows/prefactor_calibrator/bp.cwl
+++ b/workflows/prefactor_calibrator/bp.cwl
@@ -1,16 +1,18 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: bp
label: BP
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: max_separation_arcmin
- type: float
+ type: float?
+ default: ''
'sbg:x': -1000
'sbg:y': -800
- id: calibrator_name
- type: string
+ type: string?
+ default: 'POINTING'
'sbg:x': -1000
'sbg:y': -700
- id: ampRange
@@ -19,18 +21,22 @@ inputs:
'sbg:y': -600
- id: skipInternational
type: boolean?
+ default: true
'sbg:x': -1000
'sbg:y': -500
- id: max2interpolate
type: int?
+ default: 30
'sbg:x': -1000
'sbg:y': -400
- id: bandpass_freqresolution
- type: string
+ type: string?
+ default: '195.3125kHz'
'sbg:x': -1000
'sbg:y': -300
- id: avg_freqresolution
type: string?
+ default: '48.82kHz'
'sbg:x': -1000
'sbg:y': -200
- id: flagunconverged
@@ -70,14 +76,17 @@ inputs:
'sbg:y': 600
- id: antennas2transfer
type: string?
+ default: '[FUSPID].*'
'sbg:x': -1000
'sbg:y': 700
- id: do_transfer
type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': 800
- id: trusted_sources
type: string?
+ default: '3C48,3C147,3C196,3C295,3C380'
'sbg:x': -1000
'sbg:y': 900
outputs:
@@ -90,7 +99,7 @@ outputs:
- id: final_flags_join_out
outputSource:
- final_flags_join/flagged_fraction_antenna
- type: File?
+ type: File
'sbg:x': 1000
'sbg:y': -100
- id: inspection
@@ -101,7 +110,7 @@ outputs:
- losoto_plot_B2/output_plots
- losoto_plot_B3/output_plots
- transfer_solutions/plots
- type: 'File[]?'
+ type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 1000
'sbg:y': 0
@@ -615,4 +624,4 @@ steps:
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- - class: MultipleInputFeatureRequirement
+ - class: MultipleInputFeatureRequirement
\ No newline at end of file
diff --git a/workflows/prefactor_calibrator/fr.cwl b/workflows/prefactor_calibrator/fr.cwl
index dbb17414..6b9323fa 100644
--- a/workflows/prefactor_calibrator/fr.cwl
+++ b/workflows/prefactor_calibrator/fr.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: fr
label: FR
$namespaces:
@@ -25,6 +25,7 @@ inputs:
'sbg:y': 0
- id: refant
type: string?
+ default: 'CS001HBA0'
'sbg:x': -1000
'sbg:y': 100
- id: inh5parm_logfile
@@ -362,4 +363,4 @@ steps:
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- - class: MultipleInputFeatureRequirement
+ - class: MultipleInputFeatureRequirement
\ No newline at end of file
diff --git a/workflows/prefactor_calibrator/ion.cwl b/workflows/prefactor_calibrator/ion.cwl
index 956b322c..ba915404 100644
--- a/workflows/prefactor_calibrator/ion.cwl
+++ b/workflows/prefactor_calibrator/ion.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: ion
label: ion
$namespaces:
@@ -27,19 +27,23 @@ inputs:
'sbg:x': -1000
'sbg:y': -300
- id: calibrator_name
- type: string
+ type: string?
+ default: 'POINTING'
'sbg:x': -1000
'sbg:y': -200
- id: clock_smooth
- type: boolean
+ type: boolean?
+ default: true
'sbg:x': -1000
'sbg:y': -100
- id: ion_3rd
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': 0
- id: refant
type: string?
+ default: 'CS001HBA0'
'sbg:x': -1000
'sbg:y': 100
- id: h5parm
@@ -47,7 +51,8 @@ inputs:
'sbg:x': -1000
'sbg:y': 200
- id: tables2export
- type: string
+ type: string?
+ default: 'clock'
'sbg:x': -1000
'sbg:y': 300
- id: inh5parm_logfile
@@ -55,7 +60,8 @@ inputs:
'sbg:x': -1000
'sbg:y': 400
- id: maxStddev
- type: float
+ type: float?
+ default: -1.0
'sbg:x': -1000
'sbg:y': 500
- id: insolutions
@@ -80,7 +86,7 @@ outputs:
- losoto_plot_tec3rd/output_plots
- losoto_plot_clock/output_plots
- losoto_plot_Pr/output_plots
- type: 'File[]?'
+ type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 1000
'sbg:y': 0
diff --git a/workflows/prefactor_calibrator/pa.cwl b/workflows/prefactor_calibrator/pa.cwl
index fa1d3eab..bf664793 100644
--- a/workflows/prefactor_calibrator/pa.cwl
+++ b/workflows/prefactor_calibrator/pa.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: pa
label: PA
$namespaces:
@@ -25,6 +25,7 @@ inputs:
'sbg:y': 0
- id: refant
type: string?
+ default: 'CS001HBA0'
'sbg:x': -1000
'sbg:y': 100
- id: inh5parm_logfile
@@ -458,4 +459,4 @@ steps:
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- - class: MultipleInputFeatureRequirement
+ - class: MultipleInputFeatureRequirement
\ No newline at end of file
diff --git a/workflows/prefactor_calibrator/prep.cwl b/workflows/prefactor_calibrator/prep.cwl
index d711b7ff..f77f3b87 100644
--- a/workflows/prefactor_calibrator/prep.cwl
+++ b/workflows/prefactor_calibrator/prep.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: prep
label: prep
$namespaces:
@@ -10,23 +10,28 @@ inputs:
'sbg:x': -515.1839599609375
'sbg:y': 330.674560546875
- id: filter_baselines
- type: string
+ type: string?
+ default: '*&'
'sbg:x': 254.234375
'sbg:y': 684
- id: raw_data
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': 0
'sbg:y': 563
- id: propagatesolutions
- type: boolean
+ type: boolean?
+ default: true
'sbg:x': 0
'sbg:y': 670
- id: flagunconverged
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': 559.319091796875
'sbg:y': 837.5
- id: demix
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': 254.234375
'sbg:y': 1326
- id: max_dppp_threads
@@ -35,51 +40,63 @@ inputs:
'sbg:x': 254.234375
'sbg:y': 214
- id: memoryperc
- type: int
+ type: int?
+ default: 20
'sbg:x': 254.234375
'sbg:y': 107
- id: flag_baselines
- type: 'string[]'
+ type: 'string[]?'
+ default: []
'sbg:x': 254.234375
'sbg:y': 442
- id: avg_timeresolution
- type: float
+ type: int?
+ default: 4
'sbg:x': 254.234375
'sbg:y': 1554
- id: avg_freqresolution
- type: string
+ type: string?
+ default: '48.82kHz'
'sbg:x': 254.234375
'sbg:y': 1661
- id: process_baselines_cal
- type: string
+ type: string?
+ default: '*&'
'sbg:x': 0
'sbg:y': 777
- id: demix_timestep
- type: int
+ type: int?
+ default: 10
'sbg:x': 254.234375
'sbg:y': 898
- id: demix_freqstep
- type: int
+ type: int?
+ default: 16
'sbg:x': 254.234375
'sbg:y': 1219
- id: demix_target
- type: string
+ type: string?
+ default: ''
'sbg:x': 254.234375
'sbg:y': 1005
- id: demix_sources
- type: 'string[]'
+ type: 'string[]?'
+ default: []
'sbg:x': 254.234375
'sbg:y': 1112
- id: min_length
type: int?
+ default: 50
'sbg:x': 360
'sbg:y': 1919.42626953125
- id: overhead
type: float?
+ default: 0.8
'sbg:x': 180
'sbg:y': 1903.963134765625
- id: min_separation
type: int?
+ default: 30
'sbg:x': 0
'sbg:y': 884
- id: do_smooth
@@ -89,6 +106,7 @@ inputs:
'sbg:y': 944.5
- id: max_separation_arcmin
type: float?
+ default: 1.0
'sbg:x': 0
'sbg:y': 991
- id: calibrator_path_skymodel
@@ -100,12 +118,12 @@ inputs:
'sbg:x': 0
'sbg:y': 1205
- id: elevation
- type: string
+ type: string?
default: 0deg..15deg
'sbg:x': 254.234375
'sbg:y': 791
- id: amplmin
- type: float
+ type: float?
default: 1.e-30
'sbg:x': 254.234375
'sbg:y': 1768
@@ -128,12 +146,6 @@ outputs:
type: 'Directory[]'
'sbg:x': 1329.937255859375
'sbg:y': 663
- - id: parset
- outputSource:
- - ndppp_prep_cal/parset
- type: 'File[]'
- 'sbg:x': 1027.490966796875
- 'sbg:y': 884
- id: calibrator_name
outputSource:
- find_skymodel_cal/model_name
@@ -234,7 +246,6 @@ steps:
out:
- id: msout
- id: logfile
- - id: parset
run: ../../subworkflow/ndppp_prep_cal.cwl
label: ndppp_prep_cal
scatter:
@@ -441,4 +452,4 @@ requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
- - class: ScatterFeatureRequirement
+ - class: ScatterFeatureRequirement
\ No newline at end of file
diff --git a/workflows/prefactor_target.cwl b/workflows/prefactor_target.cwl
index d52c9781..af440e8f 100644
--- a/workflows/prefactor_target.cwl
+++ b/workflows/prefactor_target.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: prefactor_target
label: prefactor_target
$namespaces:
@@ -91,27 +91,27 @@ inputs:
'sbg:x': -1000
'sbg:y': -100
- id: apply_tec
- type: boolean
+ type: boolean?
default: false
'sbg:x': -1000
'sbg:y': 0
- id: apply_clock
- type: boolean
+ type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 100
- id: apply_phase
- type: boolean
+ type: boolean?
default: false
'sbg:x': -1000
'sbg:y': 200
- id: apply_RM
- type: boolean
+ type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 300
- id: apply_beam
- type: boolean
+ type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 400
@@ -174,7 +174,7 @@ inputs:
'sbg:x': -1000
'sbg:y': 1600
- id: avg_timeresolution
- type: float?
+ type: int?
default: 4
'sbg:x': -1000
'sbg:y': 1700
@@ -219,7 +219,7 @@ inputs:
'sbg:x': -1000
'sbg:y': 2500
- id: proxy_port
- type: string?
+ type: int?
default: null
'sbg:x': -1000
'sbg:y': 2600
@@ -557,4 +557,4 @@ steps:
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- - class: MultipleInputFeatureRequirement
+ - class: MultipleInputFeatureRequirement
\ No newline at end of file
diff --git a/workflows/prefactor_target/finalize.cwl b/workflows/prefactor_target/finalize.cwl
index 08bd48c6..f3f032bb 100644
--- a/workflows/prefactor_target/finalize.cwl
+++ b/workflows/prefactor_target/finalize.cwl
@@ -1,20 +1,23 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: finalize
label: finalize
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: demix_sources
- type: 'string[]'
+ type: 'string[]?'
+ default: []
'sbg:x': -1000
'sbg:y': -700
- id: demix
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': -600
- id: clip_sources
- type: 'string[]'
+ type: 'string[]?'
+ default: []
'sbg:x': -1000
'sbg:y': -500
- id: msin
@@ -30,15 +33,18 @@ inputs:
'sbg:x': -1000
'sbg:y': -200
- id: gsmcal_step
- type: string
+ type: string?
+ default: 'phase'
'sbg:x': -1000
'sbg:y': -100
- id: process_baselines_target
- type: string
+ type: string?
+ default: '[CR]S*&'
'sbg:x': -1000
'sbg:y': 0
- id: bad_antennas
- type: string
+ type: string?
+ default: '[CR]S*&'
'sbg:x': -1000
'sbg:y': 100
- id: insolutions
@@ -46,15 +52,18 @@ inputs:
'sbg:x': -1000
'sbg:y': 200
- id: compression_bitrate
- type: int
+ type: int?
+ default: 16
'sbg:x': -1000
'sbg:y': 300
- id: skymodel_source
- type: string
+ type: string?
+ default: 'TGSS'
'sbg:x': -1000
'sbg:y': 400
- id: total_bandwidth
- type: int
+ type: int?
+ default: 50
'sbg:x': -1000
'sbg:y': 500
- id: check_Ateam_separation.json
@@ -62,11 +71,13 @@ inputs:
'sbg:x': -1000
'sbg:y': 600
- id: filter_baselines
- type: string
+ type: string?
+ default: '[CR]S*&'
'sbg:x': -1000
'sbg:y': 700
- id: compare_stations_filter
- type: string
+ type: string?
+ default: '[CR]S*&'
'sbg:x': -1000
'sbg:y': 800
- id: flags
@@ -108,7 +119,7 @@ outputs:
- structure_function/structure_plot
- wsclean/image
- uvplot/output_image
- type: 'File[]?'
+ type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 1300
'sbg:y': 500
diff --git a/workflows/prefactor_target/gsmcal.cwl b/workflows/prefactor_target/gsmcal.cwl
index 48bb1606..0dac9b71 100644
--- a/workflows/prefactor_target/gsmcal.cwl
+++ b/workflows/prefactor_target/gsmcal.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: gsmcal
label: gsmcal
$namespaces:
@@ -10,20 +10,23 @@ inputs:
'sbg:x': -1000
'sbg:y': -400
- id: filter_baselines
- type: string
+ type: string?
+ default: '[CR]S*&'
'sbg:x': -1000
'sbg:y': -300
- id: num_SBs_per_group
- type: int
+ type: int?
+ default: 10
'sbg:x': -1000
'sbg:y': -200
- id: reference_stationSB
- type: int
+ type: int?
default: null
'sbg:x': -1000
'sbg:y': -100
- id: use_target
- type: boolean
+ type: boolean?
+ default: true
'sbg:x': -1000
'sbg:y': 0
- id: target_skymodel
@@ -31,31 +34,38 @@ inputs:
'sbg:x': -1000
'sbg:y': 100
- id: skymodel_source
- type: string
+ type: string?
+ default: 'TGSS'
'sbg:x': -1000
'sbg:y': 200
- id: do_smooth
- type: boolean
+ type: boolean?
+ default: false
'sbg:x': -1000
'sbg:y': 300
- id: propagatesolutions
- type: boolean
+ type: boolean?
+ default: true
'sbg:x': -1000
'sbg:y': 400
- id: avg_timeresolution_concat
- type: int
+ type: int?
+ default: 8
'sbg:x': -1000
'sbg:y': 500
- id: avg_freqresolution_concat
- type: string
+ type: string?
+ default: '97.64kHz'
'sbg:x': -1000
'sbg:y': 600
- id: min_unflagged_fraction
- type: float
+ type: float?
+ default: 0.5
'sbg:x': -1000
'sbg:y': 700
- id: refant
- type: string
+ type: string?
+ default: 'CS001HBA0'
'sbg:x': -1000
'sbg:y': 800
- id: min_length
@@ -65,7 +75,7 @@ inputs:
'sbg:y': 900
- id: overhead
type: float?
- default: 0.7
+ default: 0.8
'sbg:x': -1000
'sbg:y': 1000
outputs:
diff --git a/workflows/prefactor_target/prep.cwl b/workflows/prefactor_target/prep.cwl
index 4f46e388..802954d3 100644
--- a/workflows/prefactor_target/prep.cwl
+++ b/workflows/prefactor_target/prep.cwl
@@ -1,5 +1,5 @@
class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
id: prep
label: prep
$namespaces:
@@ -75,27 +75,27 @@ inputs:
'sbg:x': -1000
'sbg:y': -500
- id: apply_tec
- type: boolean
+ type: boolean?
default: false
'sbg:x': -1000
'sbg:y': -400
- id: apply_clock
- type: boolean
+ type: boolean?
default: true
'sbg:x': -1000
'sbg:y': -300
- id: apply_phase
- type: boolean
+ type: boolean?
default: false
'sbg:x': -1000
'sbg:y': -200
- id: apply_RM
- type: boolean
+ type: boolean?
default: true
'sbg:x': -1000
'sbg:y': -100
- id: apply_beam
- type: boolean
+ type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 0
@@ -129,7 +129,7 @@ inputs:
'sbg:x': -1000
'sbg:y': 600
- id: avg_timeresolution
- type: float?
+ type: int?
default: 4
'sbg:x': -1000
'sbg:y': 700
@@ -174,12 +174,12 @@ inputs:
'sbg:x': -1000
'sbg:y': 1500
- id: elevation
- type: string
+ type: string?
default: 0deg..15deg
'sbg:x': -1000
'sbg:y': 1600
- id: amplmin
- type: float
+ type: float?
default: 1.e-30
'sbg:x': -1000
'sbg:y': 1700
@@ -189,7 +189,7 @@ outputs:
- compare_station_list/filter_out
type: string
'sbg:x': 1000
- 'sbg:y': -800
+ 'sbg:y': -800
- id: outh5parm
outputSource:
- createRMh5parm/h5parmout
@@ -201,7 +201,7 @@ outputs:
- check_ateam_separation/output_imag
- losoto_plot_RM/output_plots
- plot_Ateamclipper/output_imag
- type: 'File[]?'
+ type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 1000
'sbg:y': -300
@@ -233,7 +233,7 @@ outputs:
- id: prep_flags_join_out
outputSource:
- prep_flags_join/flagged_fraction_antenna
- type: File?
+ type: File
'sbg:x': 1000
'sbg:y': 1100
steps:
@@ -245,9 +245,11 @@ steps:
- id: filter_station
default: ''
- id: state
- default: 'prep'
+ default: prep
out:
+ - id: refant
- id: flagged_fraction_antenna
+ - id: logfile
run: ./../../steps/findRefAnt_join.cwl
label: prep_flags_join
'sbg:x': 400
@@ -275,7 +277,7 @@ steps:
- id: h5parmdb
source: cal_solutions
- id: solset_name
- default: 'calibrator'
+ default: calibrator
- id: filter
source: filter_baselines
out:
@@ -351,15 +353,9 @@ steps:
'sbg:y': -300
- id: dppp_prep_target
in:
- - id: msin
- linkMerge: merge_flattened
- source:
- - msin
- - id: msin_baseline
- default: '*'
- source: compare_station_list/filter_out
- id: baselines_to_flag
- source: flag_baselines
+ source:
+ - flag_baselines
- id: elevation_to_flag
source: elevation
- id: min_amplitude_to_flag
@@ -373,6 +369,10 @@ steps:
- id: demix
default: false
source: demix
+ - id: msin
+ linkMerge: merge_flattened
+ source:
+ - msin
- id: skymodel
source: make_sourcedb_ateam/sourcedb
- id: timeresolution
@@ -401,34 +401,34 @@ steps:
- id: parmdb
source: createRMh5parm/h5parmout
- id: apply_tec_correction
- source: apply_tec
default: false
+ source: apply_tec
- id: apply_rm_correction
- source: apply_RM
default: true
+ source: apply_RM
- id: apply_phase_correction
- source: apply_phase
default: false
+ source: apply_phase
- id: apply_clock_correction
- source: apply_clock
default: true
+ source: apply_clock
- id: apply_beam_correction
- source: apply_beam
default: true
+ source: apply_beam
- id: filter_baselines
source: compare_station_list/filter_out
- id: updateweights
source: updateweights
- id: clip_sources
- source: clip_sources
+ source:
+ - clip_sources
out:
- - id: msout
+ - id: prep_flags_out
- id: prep_logfile
- id: predict_logfile
- id: clipper_logfile
+ - id: msout
- id: clipper_output
- - id: prep_flags_out
- - id: parset
run: ../../subworkflow/ndppp_prep_targ.cwl
label: ndppp_prep_target
scatter:
@@ -449,7 +449,8 @@ steps:
in:
- id: file_list
linkMerge: merge_flattened
- source: dppp_prep_target/clipper_output
+ source:
+ - dppp_prep_target/clipper_output
- id: file_prefix
default: Ateamclipper
- id: file_suffix
@@ -464,7 +465,8 @@ steps:
in:
- id: file_list
linkMerge: merge_flattened
- source: dppp_prep_target/prep_logfile
+ source:
+ - dppp_prep_target/prep_logfile
- id: file_prefix
default: ndppp_prep_targ
out:
@@ -477,7 +479,8 @@ steps:
in:
- id: file_list
linkMerge: merge_flattened
- source: dppp_prep_target/predict_logfile
+ source:
+ - dppp_prep_target/predict_logfile
- id: file_prefix
default: predict_targ
out:
@@ -490,7 +493,8 @@ steps:
in:
- id: file_list
linkMerge: merge_flattened
- source: dppp_prep_target/clipper_logfile
+ source:
+ - dppp_prep_target/clipper_logfile
- id: file_prefix
default: Ateamclipper
out:
@@ -529,4 +533,6 @@ steps:
'sbg:x': 400
'sbg:y': 700
requirements:
- - class: ScatterFeatureRequirement
\ No newline at end of file
+ - class: SubworkflowFeatureRequirement
+ - class: ScatterFeatureRequirement
+ - class: MultipleInputFeatureRequirement
\ No newline at end of file
--
GitLab