diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 78127616401875e4cb1a48233b21e10c75cfa25d..6c18e4449e4dd4da294039d5af203f4fcbd19f97 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 fb45f040ea7056136096c51f64b9807cc4e530c6..5be41d5e4e673aba2d403e5d67e8fc69a60442ba 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 0badc8355b972025e8dc4341cad672b7c6eee4e6..e7799b541b2224b448fb5201125e617da9333702 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 2a70f602771d7e5e669ba46ee395550807bb379d..a708ec86f1025bd2a3811e43dd5669f131152b15 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 3e0c9fde9da2eb2b577339fc8bfde8c36e00c6c8..cf339a9a147f6d56a22acde32def90243da7aaa6 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 2850b977dcfc984b3bebf38f19d35166707e0b7d..2ba76d2a59ed2e20dcf289a8ee7c84f679c17d52 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 47861182c3c60b1d24f5189334dabb7bb36f0e4d..13f6fb8a853984c1b2cb01b0ed1a6c96c4ded9ee 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 c88bdd1721d9a544f872ef89f814c361eb56dee5..c7b68cd9c674ab6ec980278aeec2c8c42259631c 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 f3e2c175ced26ad327e9d56e473bbaf0039996a5..73aedd080c62df97d141f0c2b8df2b3478139430 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 a18021373b04553b9cde5e84ca8ab531ac14854a..ed3af2da8e6f96ca531faba83d8eed444e013fa9 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 0a582b27c0d351d3b8a2f1fa2a2805094dc94ad3..0b21b0471ca001c1269b5482b36ff043133a1666 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 3c1a3031ced711121601e381e73ca08303a07a6f..a12bb7f0f34ec0201a611fc24bf2e8d640aa055e 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 123fdf1e09bcddd4144728f51a13d59b8e87fee6..19fcd5a0160abc919b4464c48c4617f512e66f68 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 64cd85154761c971cb2e86655fbcfe4355a19824..94e2113b7c661f25e269c8fcb12993fd634e9e43 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 b50754a85ab040136df19917a0e01a5464e8c7c9..7876f34737e6821cc4ba895cf64f7e9d0ba967ac 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 de2ca5c7e88d6cc6cd3f30469ac689a293ef163c..40e8ccc0936d71d23046f8a574c5592641041b89 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 d5bd04038a703c3ecfbc5f07aa917892b87bd85d..73a37b127d95c4c4e7e8eb586510051a1f61ac62 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 f935adca0125043812f663d913ef039819f6a52e..8afb93659e9b3902b1508c3530bf0dc27e9bb442 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 282c7e49349cbd3857d810a95ab535e2e877cbe4..923d9e01700796239dacea9f22532af07f16573f 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 4063c788424cdc9d635e01c0d07b793abca2eec4..c8254164cfeac2a809dd5c458852aa324db635e7 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 c829143c6092d724b595ce070add1b2f97f57966..c929b997b00be61837bed502dcf1924bde753abe 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 24b16e1797bf247cb466a84bf022c2120a13c071..9f19b287955310767ce1c3b66b8c7d39289639a9 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 a62ffbde02042034b3e371d99cb80ccb279be6f6..2c4937ecbd3dd0d6a398c6577091fe6ca67e56b1 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 aca07b9557042c5c3105ebedbcd6b6da5d339c19..fb5d2bf1ed9964dc71a6eb4de594f04a4350fa16 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 2cfd5a6a40b9cf9260ed8f33bc30c843e8450c3a..b4c2981a6568ee58a938fa9f652019479b1b1652 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 2cb7b61755263fc8a9947fb2b6538df7e514569b..86479c7454f92f9b4a3249d0fb79fe0ed02f0f5d 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 4fd0a4c6c930a99bd0fe045e9fb636b4a35a905f..2e34c03a93ac2eb7a125337b1262b1aab2845313 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 113a938d47027f73820ce7f5223f0c8ea9ec9ff0..cbcede11bc8ce062d45bfe5a9bbc9b5f62bde73a 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 78cdb67f5570cc8dcd127b91b170bb8fbcf80d67..e6b7fa9d7db6b1849070ed17e9b0e80629ffcc4f 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 01a4634f8b3e2624c93b1062022a26f775e479f6..4ea38f4f4b488051ca983a7072fef8366e27c1cc 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 dcc7b02acd8c9e454316515b73b29b0d447a5c76..61d9b09ac225508200ffd7faa36fe436266c2053 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 33e23bb71ab785443fe99f2cf503911d3b05ce24..1d3be1a78d4d39c7ab27bf45849905ea0cb9e0c4 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 e480374d9096a84da231cf0d6bfa168cdc051498..ac46bdf9efd62f65e3a96e4f41f860380846e5ef 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 b4b87b1d0b398d21a3c8e0e775acc7d372012908..ec6e1c14df0cd7eae3a453840cd5baed46fb6098 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 7d00a0c6502aaf1850841739f1564f1f52fe0ed8..1d66ef6582c427d99d93322f2f927c83314501a4 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 81bf21ddee6484295541617490fa2247c86719e6..570179108c15c30616e8b2277329ffcf475792d8 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 21f451c9308cf60ca03b1c78d9472a6d388b561c..26ae49cd04ae23bf565fe5159711fd1679d0c52f 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 b0d274ff9d60be6619699fea3b08a77b26326889..8df7c04696ed2e1234e07c3cef48529362040118 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 f07e29e581b655b1ca098c7d15013e560d22a845..29ab625bb313fad536210876695f30673d21dd27 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 27004fb432c37393000524bbe4a8cf1a7c5c95c6..5e16f93c4922f6918a37d876cd2273056e29dce9 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 e8ba30cac630b70d79499edf7bc20d9db594eaa1..4a54161f872fcee0702b779d2c8487709489c283 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 b2a1fb6b678cc6d63c6ebc384f21a4d56b222a22..14e02ccb29528fd18007654bf2a1d130ac89d029 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 1a0fa547154e818c29f47c3795a69838fae74c5a..7ab1a0de4e1936163a47186c87c6a498e83a70ff 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 33cee0a343f4ccb545220fd6945918c61b1b0e61..3ec0fdd37a64525aae00d5ead4803f49191348a0 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 deb8446669c6fbdd93d188fde54b64c6e82ca89c..06f5e0b7ac6314ebdbebeea7bbfb69b80a6b563f 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 a167095c3825a2dcb64bf7c66f95e1991d35cdcc..fd35fe5cbec0c3a4069379bb600e1b7ad20db5a4 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 43ed10b9507b78c7c4724b959ec215589c6405d4..4f1a9c390ab6040e087db745a28469fb0a69644a 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 8fe2290cb2b3b44cd48350a4db296fd96798d0bf..9fd3604f2f228e2f76e3e273325605ed7995430a 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 64a39c072074d096e708fd5b78137bfe2ca0b9ab..e069f929ba6f07f760bc1d0ca575774bc34c83ce 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 e749346fc737b1d2de4d5fbc07c9435edf1477dd..1cccdaef17ef7abe6ab256f9b32b476717d4e438 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 bc9a36ee54a9444d3c2f4c8d009bf4dc870f67bb..78ad7078e8e3361074a12bcac24c805d93567f24 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 3a11c723cf4e08e39618dcf4cc060828227c5e94..e92b2b0d31f820a4d3ce89dd2a84687660e01f88 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 1ff03cbb02ace1d645d5787856dfb8281643bb6a..5b39b048bce5218a1e69a2b2cc0f57bb08ccd10e 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 fab5d2a548b4fd2be1f9f0e91ee50ef09d8bf8fb..44e5c96b927667d1c78c7543466654acf66b8b88 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 bd07094507da39c52268eb3c10f739df132f8f2c..22e5dd97078679bbf060896537dcdaffa2d11d36 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 d3406adeb126e8fb920fa70b83e727d6abf3c8d1..90e2d29507b4088d4ffc3fd49a0774ddbdd90b44 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 5370829be0754975a110d9074ededbefe6799d3e..9fb3c591cb8a5a592ae2a510bf3d84d257a41025 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 4f6c03a5e30790a364e4981a3499699cbcf4119b..04e259d17c0da229b39770ccdaf2af9928cf864f 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 6f4efd6b3d68a7cb7d1e7a37948af1bcc80a9aad..072d088e3189b128c1d56d9dd76dd00f1dcac2f8 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 9102a16c2b80e11c577082a1b0f2498319eb2779..cb456fb8c59477b6a32fced5a946b6b487271ae8 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 911dfb45a99f03a1e73664ffd96711a37aa7b757..32908f0e53b9b19db2cac60c5b8690b027c54b54 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 5790c430dfe0436020c7607baf153fd9454c01c4..3848b0067d9dca0c329af3f80e618b33e02ab789 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 ab5987b158461486c26fd1c3f6066c54c4136ffa..b7dc32b3e411dfd5c45602373a768029453ca975 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 7c1b5414e3e458085657a98ddfd455fcb0a0ce2d..75e1f90668b33b45273a40246f3167044237c896 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 e3f5bdac0a5e03c744726b23699baf0c3834a212..3b874498aee0de61f8b0698de1d6bde9d4b1b1ed 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 06c9859332945aec904e964e4d7003d50be0443d..60de7379922aec4b15f418dcbeb5e83991010390 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 505eecf6aa537f5e59391e59a1e3d46f7deaec71..10b25bc5bb2dd8a4a5aba5bfa69878fbb5520760 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 73301837e0eb8d7a5f0e9495e14e61bd8962af86..7c6763bf408b40a2a00ff174ae97266af8d89fb4 100644
--- a/steps/directory_listing.cwl
+++ b/steps/directory_listing.cwl
@@ -1,5 +1,5 @@
class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: directory_listing
diff --git a/steps/dppp_make_parset_cal.cwl b/steps/dppp_make_parset_cal.cwl
new file mode 100755
index 0000000000000000000000000000000000000000..bb6fbfddea240eecd6828377a4005c1cdc9a6f69
--- /dev/null
+++ b/steps/dppp_make_parset_cal.cwl
@@ -0,0 +1,117 @@
+class: CommandLineTool
+cwlVersion: v1.1
+id: make_parset
+label: define_parset
+$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 = $(inputs.ntimechunk)
+ demix.freqstep = 1
+ demix.timestep = 1
+ demix.instrumentmodel = instrument
diff --git a/steps/dppp_make_parset_target.cwl b/steps/dppp_make_parset_target.cwl
new file mode 100755
index 0000000000000000000000000000000000000000..f31c0a84e56f840adbc301c1be1a17c8afeee024
--- /dev/null
+++ b/steps/dppp_make_parset_target.cwl
@@ -0,0 +1,166 @@
+class: CommandLineTool
+cwlVersion: v1.1
+id: make_parset
+label: define_parset
+$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 = $(inputs.ntimechunk)
+ demix.freqstep = 1
+ demix.timestep = 1
+ demix.instrumentmodel = instrument
diff --git a/steps/dppp_prep_cal.cwl b/steps/dppp_prep_cal.cwl
new file mode 100755
index 0000000000000000000000000000000000000000..e8d9dda6ae516669345e6eae3fe2b321ba8df70a
--- /dev/null
+++ b/steps/dppp_prep_cal.cwl
@@ -0,0 +1,103 @@
+class: CommandLineTool
+cwlVersion: v1.1
+$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: $(inputs.msin)
+ writable: true
diff --git a/steps/dppp_prep_target.cwl b/steps/dppp_prep_target.cwl
new file mode 100755
index 0000000000000000000000000000000000000000..fa9060db56fe0ac420e2487ea376833c1db3d0cd
--- /dev/null
+++ b/steps/dppp_prep_target.cwl
@@ -0,0 +1,141 @@
+class: CommandLineTool
+cwlVersion: v1.1
+$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 e09eec16771c5130b0c896db0ce86b4b48818903..2d1f569256aa2f7a5d76ef4336ba545aedced1ba 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 d4544091d58cb7c982648708896b780b282fdbfd..77c842ea81b6ad680ac861b67c6c4d4c0f45bc02 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 e8ffabc885bc687a81010e3584d3fe8a74b1d6da..c59160190e339be2a3e92e6900738494d29c5ed2 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 7ee4e7efc4f04a475956b5339a96113511889fa4..89b5997a3057b016e647c74e3573e9810dbda123 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 fcc32d18a0856d0c1ce79689bd0f7717b9288ac8..b9c22a2f902f3087f96d37f5cfeeb00d09e0506c 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 0bfa0572d6301eb6c84c95b0adbb16fc5d6520ae..491bf3fe9b646706d21fc09f8b37d4c29a2ac299 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 e1a99a389985b84f9448ae14ddc53c4601e1d353..06c90242f80b1a246f35ffddf784a8a32249a19f 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 fdf076b5e1956db9aeb63fff012c102b5c1e0899..36b62037adbeca6b1d1906b8c85aebfb9e92283e 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 1a2409abcd9236456fee5e0d7e81e62143670a28..1f7b6630e5e368fae30578acc3e2087aa17599df 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 8d2abd592872fa258946b480e05cdcd4e1b57481..52042229ba579e5000516f72bcfc7835820c89a7 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 7d8fef0a75749789ad62c9fdd4840fc9ce17a986..14fcd046bb4072028b3cc5de584575b0e002f7e8 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 c4c5c6122e03f690e2bcf14307ec052f4d846f86..2ad56843e005f39413631142495d40a9090f8182 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 c9e198210122c159ac4c18f06294c4e8a1e444c5..188972edca324f8669691073d33f9f86ac08ea0e 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 48047a01e3961438155ace02311eddc850308039..015d6ba7c3eea5a7fb13b7a0139eeaee1097c27d 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 b1527d08845a46d2bc037dc98084d4fb8b7a85b3..43c7a42c2026956393e6804d2530aaeeffb3f325 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 c4ecb01874588d841d2080a853e0ee6f8d716619..3175f9d69af65cedaecff458646a96765ef52862 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 b928a3ffdc95e6ded6dfa0bd9f11db36500900bd..d2a668e7f2c9af4c52bf147726d1ddd30e7e0ec3 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 a5e1389e9b7498126e78973a4f8637e41eecf55b..7bbb37f402d7a4059fb3aa388c98cd3d39f1df06 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 3c3c14f835a78e9e4bc6f52fc8787eb8cb24de6a..4bf3c815ab15b0960a1ec9750c1332db9afeb8a2 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 0cc4266af5f67fb477e425d90e9055525473b2e4..7520bfdc1a276d7691e1de1bf381ae8b7175f395 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 bc1383670481798201b56383b82d97f2c196ca6e..756129e7aa1d86237c12b1f077a701a9e8fd8448 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 809299e1c578b10bb3363d6bb8b9710bfe43cabd..bc3075ccb197e4514d1ea7b4664bc46f58ba107b 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 08bd4527548054a827a951a02f5948ce596598fa..15e45420801c68d56dd720063ccc3fcf56c2ee0e 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 d58d3145c8cbb716e53940a6c91a828b2b96b361..1296467da15c4d0c633b2cfe77a7068209215d01 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 55d02a9d7e4d3b154312c21c7ef6980d6410ccb8..0ca0dcf00abc2a9903061e4e7e80df313efeda33 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 34a2a2aaa7821f20f115f6ef7672b380d8bcb2c1..05f7fddab89af0b0593af4fddef51c360a3464d5 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 de5863ce7ef4f7b3c374d25960533cd07bde3a1e..e0e70ea93355022e557ed41ee28d02ac3b53163c 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 3c20638a5f7dfa43e0c60c18ab97eb6a1f193898..1350e1c90e6989f283b213b93fad8ddebfa832e3 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 c8f1ea5cf33df4b2e381e0357129676db82147db..6fb98eb1210ee4536a5f9f960f264ca93a87706c 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 7f6af5ac4412abde5b945d1e2efa6745e19ef70e..f5ff47d8d1988a31475e1ee25886be172c281d1e 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 63f7dc6355cfdbe1cbf68ffe531c192b9eaf637b..1d0f2bd02c2a679d356425df432aa0f0a15c9aae 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 1fceb82d5f227d8243c7b89d8d4d05a291cea5da..d2c09a9fc9feb645a59e6aa449b1519bc71d2b89 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 5ff661bbd13c4c1894795283e94696a697af4a15..b09da67e2e78dcc2bc58f68c3cd75e64e17a6407 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 66c856942b9725f03c02120b3cd89002dbf4cc7c..6dedf0a6375cf73846ac58f04be8573a02e36976 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 d2224d3459a8bf5297e408f2bce09a9dd4e3085b..a7a3eb0c347219bbd539ac265a1989ffe0438f82 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 7afd26b6adc4e93c0c2c385554bf3b653465ab21..350378d404d047c47c9859b40e9e78c4ae946535 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 4d8ccac1a5e246c3d3842dff3009f47f8a326f7d..8b1b755af33a04c9ce7f56e269e3bdb2d4233659 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 4b668f7b7ce12a649075edd973c99d801699cf3a..b1771a09821fd788aef17bf98fb16c864301f72a 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 3eec42be91dd785d0ea254ebef3fd13925672156..408f975418d4a8297b742ab63a081151b3eea9a5 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 6bcdf446b3a632500708dabb251e23deb0820aa6..8f46bd8d948e020d0a66c928964f02f83b2c1fef 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 f40d3ad325d74958e85d2202722f28203ce1034e..e68210685bd0efef96083c1a33bbe5af69cf2803 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 ee2d7dbd423bec7b6b0e1d97b3412f01c38ee105..b354b0458ae7f1cb5071426a938e7840ab4499bb 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 4186dd11968ae6f8bb8e95aa1bf9f54f4b133562..b212217d880e42a4717a1d6540975588f83a6857 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 040369920b72fbd5c472c93555fa2532d0b9075d..ae613386cd48ac520b3e219f033294caf75471a1 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 8995c3b085b287a47dfb7cbe892c854bf2bb1366..bae17b5525665bffb380b5ed5e48d23bb4241a52 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 4318c4753d204a63adde9222d3c2ed0c510678e9..e1cea47d542341b6d8585cd6e33e4d5e06a8de45 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 2ce25bceb0c5536167063f9730569acf12b9b1ef..ad364596d2772c98c1ffba52607c55c1d94cef34 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 5ab2a692fd5124a6ab0d502b7cc1873dd8e669d9..366f9c5aff501119792cb67507dce8067d696279 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 3cf5b624dd834090428b166d66df6b4392b4c342..debd64a89e7591a60371424dba36c0b677dfcb4e 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 1970c508c382c3bf9a614ca78c678136530df2d7..9234a4e8ed973052d8d4c27a79c5bb5413002443 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 921a3be57946b7287cc5cbf9de2f24e3ade8bff1..0c9343cae03054c0c0bf24d98d7eb7a9045f699a 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 02f0143c543283bcbd48b6853e2dc1f70eebdc62..cc06d7ea5327475b8d7034202355f6795bc355c4 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 906d905d83090627f8842ff00eb1e59bca522e26..c305f321a2a1684b8dce5f13437b65ea4cea3bbe 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 d5d1399ca570eb7c0c06cd30501c525b3811f533..3c29be6e07d05b09cc0c41bc4b6c50e289eb1ae0 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 328385f3b8dc90e93f9bdf58a94950ec09671fc4..c3490d7867819ac630d8071ca1e499710d1ee361 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 ded68950f95d3ac652f50f751a520f534def8f49..13e75238777ccdae31755c0100a81bc46bb6b40f 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 1a43352a5941e0fc907c24d63ddba2c72dff2421..9a4328a3d8ecab33275a43e2bc83339dac6cae86 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 dbb17414c51f0b76454133888aaf30a6fef212ef..6b9323fa392891c6a967ad1e15a8ae5a4cd7b908 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 956b322cbbc173376e2e427c4fc504298d49f4b8..ba9154042a8bc80bd389068ccf6277bc6d3166a5 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 fa1d3eabf48540a8a42147a76573a587eebee5b3..bf664793ee6c79a2c6d05723a7179b3447e77082 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 d711b7ff19169f979e6910d1d1ff5ae953e9653c..f77f3b870f1eb08534231f207b9aebe64a918d42 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 d52c978104bdf52c4efbc326a59a64b2d472293c..af440e8f18ce96cc1c0f0ccfa97d85c27929a2ec 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 08bd48c65cd80e80e9bcae32151f0b7d4f7be97a..f3f032bbd544905c2c5e77533e2766e2cb97f3c0 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 48bb1606ad5123afbf31e314372d37ecca7c8121..0dac9b7143421e27659a015eb0b398551ec20260 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 4f46e388f17d7e7b6cfbcb620f5a1777a5fb3a0d..802954d3471b96ed98cc2ab42d599ea63cc3c913 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