diff --git a/lofar-cwl/steps/check_ateam_separation.cwl b/lofar-cwl/steps/check_ateam_separation.cwl
index 516beb6100f9e73b06cef498a05fc64ae74bd101..c8d801c94a6e32aac1ea6ba83a8d2687448baf22 100755
--- a/lofar-cwl/steps/check_ateam_separation.cwl
+++ b/lofar-cwl/steps/check_ateam_separation.cwl
@@ -1,7 +1,5 @@
class: CommandLineTool
cwlVersion: v1.0
-$namespaces:
- sbg: 'https://www.sevenbridges.com/'
id: check_ateam_separation
baseCommand:
- python3
diff --git a/steps/copy_in_one_directory.cwl b/steps/copy_in_one_directory.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..16a2be68216aeca55603c642fe6af3552b813630
--- /dev/null
+++ b/steps/copy_in_one_directory.cwl
@@ -0,0 +1,27 @@
+id: copy_in_one_directory
+label: copy_in_one_directory
+class: ExpressionTool
+
+cwlVersion: v1.0
+inputs:
+ - id: input
+ type: Directory[]
+outputs:
+ - id: output
+ type: Directory
+ glob: .
+
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - $(inputs.input)
+
+
+expression: |
+ ${
+
+ }
+
+
+requirements:
+ - class: InlineJavascriptRequirement
diff --git a/workflows/HBA_calibrator.cwl b/workflows/HBA_calibrator.cwl
index 7bc2d98a374371cbab694c0483eac24d366f7c21..46f8891cbf2b0e837bf8464446b1c2c4a853160a 100644
--- a/workflows/HBA_calibrator.cwl
+++ b/workflows/HBA_calibrator.cwl
@@ -344,9 +344,6 @@ steps:
label: save_results
'sbg:x': 1200
'sbg:y': 0
-hints:
- cwltool:LoadListingRequirement:
- loadListing: shallow_listing
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
diff --git a/workflows/dowload_surl_and_create_input_file-json.cwl b/workflows/dowload_surl_and_create_input_file-json.cwl
index 55a5b3305e4fe4fa2d2b709b1d6c4d57d38d6759..328385f3b8dc90e93f9bdf58a94950ec09671fc4 100644
--- a/workflows/dowload_surl_and_create_input_file-json.cwl
+++ b/workflows/dowload_surl_and_create_input_file-json.cwl
@@ -2,26 +2,19 @@ class: Workflow
cwlVersion: v1.0
id: dowload_surl_and_create_input_file_json
label: dowload_surl_and_create_input_file.json
-$namespaces:
- sbg: 'https://www.sevenbridges.com/'
+
inputs:
- id: surl_list
type: File
- 'sbg:x': -329.7890625
- 'sbg:y': -35
outputs:
- id: results
outputSource:
- _h_b_a_calibrator/results
type: Directory
- 'sbg:x': 739.1641235351562
- 'sbg:y': -95.5
- id: logs
outputSource:
- _h_b_a_calibrator/logs
type: Directory
- 'sbg:x': 725.1641235351562
- 'sbg:y': 153.5
steps:
- id: read_surl_list
in:
@@ -31,8 +24,6 @@ steps:
- id: surls
run: ../steps/read_surl_list.cwl
label: ReadSurlList
- 'sbg:x': -158
- 'sbg:y': -40
- id: surl_copy
in:
- id: surl
@@ -43,8 +34,6 @@ steps:
label: surl_copy
scatter:
- surl
- 'sbg:x': 145
- 'sbg:y': -19
- id: untar
in:
- id: tar_file
@@ -55,8 +44,6 @@ steps:
label: untar
scatter:
- tar_file
- 'sbg:x': 350
- 'sbg:y': 8
- id: stage
in:
- id: input
@@ -67,8 +54,6 @@ steps:
label: stage
scatter:
- input
- 'sbg:x': -8
- 'sbg:y': -29
- id: _h_b_a_calibrator
in:
- id: msin
@@ -79,8 +64,6 @@ steps:
- id: results
run: ./HBA_calibrator.cwl
label: HBA_calibrator
- 'sbg:x': 563
- 'sbg:y': 17
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
diff --git a/workflows/prefactor_calibrator/prep.cwl b/workflows/prefactor_calibrator/prep.cwl
index 7f4cdd1fbfdc8e4fa3acc6f4abe682dededf5e79..c87e9fbbb172343c81b3a8939e2bf8dc853c0532 100644
--- a/workflows/prefactor_calibrator/prep.cwl
+++ b/workflows/prefactor_calibrator/prep.cwl
@@ -7,147 +7,146 @@ $namespaces:
inputs:
- id: msin
type: 'Directory[]'
- 'sbg:x': -1000
- 'sbg:y': -900
+ 'sbg:x': -515.1839599609375
+ 'sbg:y': 330.674560546875
- id: filter_baselines
type: string
- 'sbg:x': -1000
- 'sbg:y': -800
+ 'sbg:x': 254.234375
+ 'sbg:y': 684
- id: raw_data
type: boolean
- 'sbg:x': -1000
- 'sbg:y': -700
+ 'sbg:x': 0
+ 'sbg:y': 563
- id: propagatesolutions
type: boolean
- 'sbg:x': -1000
- 'sbg:y': -600
+ 'sbg:x': 0
+ 'sbg:y': 670
- id: flagunconverged
type: boolean
- 'sbg:x': -1000
- 'sbg:y': -500
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 837.5
- id: demix
type: boolean
- 'sbg:x': -1000
- 'sbg:y': -400
+ 'sbg:x': 254.234375
+ 'sbg:y': 1326
- id: max_dppp_threads
type: int?
default: 10
- 'sbg:x': -1000
- 'sbg:y': -300
+ 'sbg:x': 254.234375
+ 'sbg:y': 214
- id: memoryperc
type: int
- 'sbg:x': -1000
- 'sbg:y': -200
+ 'sbg:x': 254.234375
+ 'sbg:y': 107
- id: flag_baselines
type: 'string[]'
- 'sbg:x': -1000
- 'sbg:y': -100
+ 'sbg:x': 254.234375
+ 'sbg:y': 442
- id: avg_timeresolution
type: float
- 'sbg:x': -1000
- 'sbg:y': 0
+ 'sbg:x': 254.234375
+ 'sbg:y': 1554
- id: avg_freqresolution
type: string
- 'sbg:x': -1000
- 'sbg:y': 100
+ 'sbg:x': 254.234375
+ 'sbg:y': 1661
- id: process_baselines_cal
type: string
- 'sbg:x': -1000
- 'sbg:y': 200
+ 'sbg:x': 0
+ 'sbg:y': 777
- id: demix_timestep
type: int
- 'sbg:x': -1000
- 'sbg:y': 300
+ 'sbg:x': 254.234375
+ 'sbg:y': 898
- id: demix_freqstep
type: int
- 'sbg:x': -1000
- 'sbg:y': 400
+ 'sbg:x': 254.234375
+ 'sbg:y': 1219
- id: demix_target
type: string
- 'sbg:x': -1000
- 'sbg:y': 500
+ 'sbg:x': 254.234375
+ 'sbg:y': 1005
- id: demix_sources
type: 'string[]'
- 'sbg:x': -1000
- 'sbg:y': 600
+ 'sbg:x': 254.234375
+ 'sbg:y': 1112
- id: min_length
type: int?
- 'sbg:x': -1000
- 'sbg:y': 700
+ 'sbg:x': 360
+ 'sbg:y': 1919.42626953125
- id: overhead
type: float?
- 'sbg:x': -1000
- 'sbg:y': 800
+ 'sbg:x': 180
+ 'sbg:y': 1903.963134765625
- id: min_separation
type: int?
- 'sbg:x': -1000
- 'sbg:y': 900
+ 'sbg:x': 0
+ 'sbg:y': 884
- id: do_smooth
type: boolean?
default: false
- 'sbg:x': -1000
- 'sbg:y': 1000
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 944.5
- id: max_separation_arcmin
type: float?
- 'sbg:x': -1000
- 'sbg:y': 1100
+ 'sbg:x': 0
+ 'sbg:y': 991
- id: calibrator_path_skymodel
type: Directory?
- 'sbg:x': -1000
- 'sbg:y': 1200
+ 'sbg:x': 0
+ 'sbg:y': 1098
- id: A-Team_skymodel
type: File?
- 'sbg:x': -1000
- 'sbg:y': 1300
+ 'sbg:x': 0
+ 'sbg:y': 1205
- id: elevation
type: string
default: 0deg..20deg
- 'sbg:x': -1000
- 'sbg:y': 1400
+ 'sbg:x': 254.234375
+ 'sbg:y': 791
- id: amplmin
type: float
default: 1.e-30
- 'sbg:x': -1000
- 'sbg:y': 1500
+ 'sbg:x': 254.234375
+ 'sbg:y': 1768
outputs:
- id: outh5parm
outputSource:
- h5parm_collector/outh5parm
type: File
- 'sbg:x': 1000
- 'sbg:y': -500
+ 'sbg:x': 1554.5106201171875
+ 'sbg:y': 884
- id: check_Ateam_separation.png
outputSource:
- check_ateam_separation/output_imag
type: File
- 'sbg:x': 1000
- 'sbg:y': -300
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 1051.5
- id: msout
outputSource:
- predict_calibrate/msout
type: 'Directory[]'
- 'sbg:x': 1000
- 'sbg:y': 0
+ 'sbg:x': 1329.937255859375
+ 'sbg:y': 663
- id: parset
outputSource:
- ndppp_prep_cal/parset
type: 'File[]'
- 'sbg:x': 1000
- 'sbg:y': 200
+ 'sbg:x': 1027.490966796875
+ 'sbg:y': 884
- id: calibrator_name
outputSource:
- find_skymodel_cal/model_name
type: string
- 'sbg:x': 1000
- 'sbg:y': 400
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 1158.5
- id: outh5parm_logfile
outputSource:
- h5parm_collector/log
- type: File[]
- 'sbg:x': 1000
- 'sbg:y': 650
+ type: 'File[]'
+ 'sbg:x': 1554.5106201171875
+ 'sbg:y': 777
- id: logfiles
- linkMerge: merge_flattened
outputSource:
- concat_logfiles_calib/output
- concat_logfiles_predict/output
@@ -158,18 +157,23 @@ outputs:
- make_sourcedb_ateam/log
- check_ateam_separation/logfile
type: 'File[]'
- 'sbg:x': 1000
- 'sbg:y': 800
+ linkMerge: merge_flattened
+ 'sbg:x': 1554.5106201171875
+ 'sbg:y': 991
steps:
- - id: ndppp_prep_cal
+ - id: copy
in:
- - id: msin
- linkMerge: merge_flattened
+ - id: input
source:
- msin
- - id: msin_baseline
- default: '*'
- source: filter_baselines
+ out:
+ - id: output
+ run: ../../steps/copy_in_one_directory.cwl
+ label: copy_in_one_directory
+ 'sbg:x': -267.1643981933594
+ 'sbg:y': 480.32098388671875
+ - id: ndppp_prep_cal
+ in:
- id: baselines_to_flag
default: []
source:
@@ -187,6 +191,13 @@ steps:
- id: demix
default: false
source: demix
+ - id: msin
+ linkMerge: merge_flattened
+ source:
+ - msin
+ - id: msin_baseline
+ default: '*'
+ source: filter_baselines
- id: skymodel
source: make_sourcedb_ateam/sourcedb
- id: timeresolution
@@ -220,8 +231,8 @@ steps:
label: ndppp_prep_cal
scatter:
- msin
- 'sbg:x': 0
- 'sbg:y': 0
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 497.5
- id: predict_calibrate
in:
- id: msin
@@ -246,13 +257,13 @@ steps:
label: predict_calibrate
scatter:
- msin
- 'sbg:x': 500
- 'sbg:y': 0
+ 'sbg:x': 1027.490966796875
+ 'sbg:y': 749
- id: check_ateam_separation
in:
- id: ms
source:
- - msin
+ - copy/output
- id: min_separation
source: min_separation
out:
@@ -260,8 +271,8 @@ steps:
- id: logfile
run: ../../lofar-cwl/steps/check_ateam_separation.cwl
label: check_Ateam_separation
- 'sbg:x': 0
- 'sbg:y': -300
+ 'sbg:x': 254.234375
+ 'sbg:y': 1440
- id: make_sourcedb_ateam
in:
- id: sky_model
@@ -273,13 +284,13 @@ steps:
- id: log
run: ../../lofar-cwl/steps/makesourcedb.cwl
label: make_sourcedb_ateam
- 'sbg:x': -500
- 'sbg:y': 300
+ 'sbg:x': 254.234375
+ 'sbg:y': 328
- id: find_skymodel_cal
in:
- id: msin
source:
- - msin
+ - copy/output
- id: skymodels
source: calibrator_path_skymodel
- id: max_separation_arcmin
@@ -290,8 +301,8 @@ steps:
- id: logfile
run: ../../steps/find_skymodel_cal.cwl
label: find_skymodel_cal
- 'sbg:x': -500
- 'sbg:y': 500
+ 'sbg:x': 254.234375
+ 'sbg:y': 563
- id: make_sourcedb
in:
- id: sky_model
@@ -303,21 +314,22 @@ steps:
- id: log
run: ../../lofar-cwl/steps/makesourcedb.cwl
label: make_sourcedb
- 'sbg:x': 0
- 'sbg:y': 500
+ 'sbg:x': 559.319091796875
+ 'sbg:y': 723.5
- id: concat_logfiles_prep_cal
in:
- id: file_list
linkMerge: merge_flattened
- source: ndppp_prep_cal/logfile
+ source:
+ - ndppp_prep_cal/logfile
- id: file_prefix
default: ndppp_prep_cal
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_prep_cal
- 'sbg:x': 250
- 'sbg:y': 300
+ 'sbg:x': 1027.490966796875
+ 'sbg:y': 991
- id: concat_logfiles_blsmooth
in:
- id: file_list
@@ -329,8 +341,8 @@ steps:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_blsmooth
- 'sbg:x': 750
- 'sbg:y': 300
+ 'sbg:x': 1329.937255859375
+ 'sbg:y': 1105
- id: concat_logfiles_predict
in:
- id: file_list
@@ -343,8 +355,8 @@ steps:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_predict
- 'sbg:x': 750
- 'sbg:y': 500
+ 'sbg:x': 1329.937255859375
+ 'sbg:y': 891
- id: concat_logfiles_calib
in:
- id: file_list
@@ -356,8 +368,8 @@ steps:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_calib
- 'sbg:x': 750
- 'sbg:y': 800
+ 'sbg:x': 1329.937255859375
+ 'sbg:y': 998
- id: h5parm_collector
in:
- id: h5parmFiles
@@ -374,8 +386,10 @@ steps:
- id: log
run: ../../lofar-cwl/steps/H5ParmCollector.cwl
label: H5parm_collector
- 'sbg:x': 750
- 'sbg:y': -300
+ 'sbg:x': 1329.937255859375
+ 'sbg:y': 777
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
+ - class: InlineJavascriptRequirement
+ - class: StepInputExpressionRequirement