Refactor workflows

subworkflow/calib_cal.cwl

@@ -47,7 +47,7 @@ steps:
         source: do_smooth
     out:
       - id: msout
-    run: ../steps/blsmooth.cwl
+    run: ../lofar-cwl/steps/blsmooth.cwl
     label: BLsmooth
     'sbg:x': -420
     'sbg:y': -26
@@ -59,7 +59,7 @@ steps:
         source: make_sourcedb/sourcedb
     out:
       - id: msout
-    run: ../steps/predict.cwl
+    run: ../lofar-cwl/steps/predict.cwl
     'sbg:x': -1
     'sbg:y': -71
   - id: find_skymodel_cal_py
@@ -70,7 +70,7 @@ steps:
         source: skymodels
     out:
       - id: output_models
-    run: ../steps/find_skymodel_cal.cwl
+    run: ../lofar-cwl/steps/find_skymodel_cal.cwl
     label: find_skymodel_cal.py
     'sbg:x': -416
     'sbg:y': -209
@@ -80,7 +80,7 @@ steps:
         source: find_skymodel_cal_py/output_models
     out:
       - id: sourcedb
-    run: ../steps/makesourcedb.cwl
+    run: ../lofar-cwl/steps/makesourcedb.cwl
     label: make_sourcedb
     'sbg:x': -221
     'sbg:y': -217
@@ -97,7 +97,7 @@ steps:
     out:
       - id: msout
       - id: h5parm
-    run: ../steps/ddecal.cwl
+    run: ../lofar-cwl/steps/ddecal.cwl
     'sbg:x': 222
     'sbg:y': -89
 requirements: []

subworkflow/ndppp_prep_cal.cwl

@@ -77,7 +77,7 @@ steps:
           - baselines_to_flag
     out:
       - id: augmented_steps
-    run: ../steps/DP3.PreflaggerStepGenerator.cwl
+    run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
     'sbg:x': 955.2450561523438
     'sbg:y': -75.71149444580078
   - id: flagelev
@@ -91,7 +91,7 @@ steps:
         source: elevation_to_flag
     out:
       - id: augmented_steps
-    run: ../steps/DP3.PreflaggerStepGenerator.cwl
+    run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
     'sbg:x': 1187.4771728515625
     'sbg:y': -83
   - id: process_raw_data_select
@@ -105,7 +105,7 @@ steps:
         default: []
     out:
       - id: selected_steps
-    run: ../steps/DP3.Selector.cwl
+    run: ../lofar-cwl/steps/DP3.Selector.cwl
     label: Selector
     'sbg:x': 621.4892578125
     'sbg:y': -71.31844329833984
@@ -120,7 +120,7 @@ steps:
         source: min_amplitude_to_flag
     out:
       - id: augmented_steps
-    run: ../steps/DP3.PreflaggerStepGenerator.cwl
+    run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
     'sbg:x': 1385.993408203125
     'sbg:y': -42.28850555419922
   - id: flagedge
@@ -133,7 +133,7 @@ steps:
         default: '[0..nchan/32-1,31*nchan/32..nchan-1]'
     out:
       - id: augmented_steps
-    run: ../steps/DP3.PreflaggerStepGenerator.cwl
+    run: ../lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
     'sbg:x': 122.25408935546875
     'sbg:y': -54.06163024902344
   - id: aoflag
@@ -149,7 +149,7 @@ steps:
         default: false
     out:
       - id: augmented_steps
-    run: ../steps/DP3.AOFlaggerStepGenerator.cwl
+    run: ../lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl
     'sbg:x': 369.9876708984375
     'sbg:y': -38.086280822753906
   - id: demix_select
@@ -164,7 +164,7 @@ steps:
           - flagamp/augmented_steps
     out:
       - id: selected_steps
-    run: ../steps/DP3.Selector.cwl
+    run: ../lofar-cwl/steps/DP3.Selector.cwl
     label: demix?
     'sbg:x': 1974.7406005859375
     'sbg:y': -32.03063201904297
@@ -179,7 +179,7 @@ steps:
         source: skymodel
     out:
       - id: augmented_steps
-    run: ../steps/DP3.DemixerStepGenerator.cwl
+    run: ../lofar-cwl/steps/DP3.DemixerStepGenerator.cwl
     'sbg:x': 1676.6593017578125
     'sbg:y': 90.7158203125
   - id: parsetgenerator
@@ -193,7 +193,7 @@ steps:
       - id: input_directories
       - id: output_file_names
       - id: output_directory_names
-    run: ../steps/DP3.ParsetGenerator.cwl
+    run: ../lofar-cwl/steps/DP3.ParsetGenerator.cwl
     'sbg:x': 2340.85400390625
     'sbg:y': -79.32791900634766
   - id: dppp
@@ -220,7 +220,7 @@ steps:
       - id: secondary_output_files
       - id: secondary_output_directories
       - id: logfile
-    run: ../steps/DPPP.cwl
+    run: ../lofar-cwl/steps/DPPP.cwl
     'sbg:x': 2669.29345703125
     'sbg:y': -42.129730224609375
   - id: average_step_generator
@@ -236,7 +236,7 @@ steps:
         source: freqresolution
     out:
       - id: augmented_steps
-    run: ../steps/DP3.AveragerStepGenerator.cwl
+    run: ../lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
     'sbg:x': 2158.297119140625
     'sbg:y': -55.93873977661133
 requirements:

workflows/prefactor_calibrator.cwl

@@ -141,7 +141,7 @@ steps:
         source: uvw
     out:
       - id: output_ms
-    run: ../steps/AOFlagger.cwl
+    run: ../lofar-cwl/steps/AOFlagger.cwl
     label: AOFlagger
     scatterMethod: flat_crossproduct
     'sbg:x': -164
@@ -181,7 +181,7 @@ steps:
     out:
       - id: outh5parm
       - id: log
-    run: ../steps/H5ParmCollector.cwl
+    run: ../lofar-cwl/steps/H5ParmCollector.cwl
     label: H5parm_collector
     'sbg:x': 292.1979675292969
     'sbg:y': -543.7208251953125
@@ -195,7 +195,7 @@ steps:
     out:
       - id: output_imag
       - id: logfile
-    run: ../steps/check_ateam_separation.cwl
+    run: ../lofar-cwl/steps/check_ateam_separation.cwl
     label: check_Ateam_separation
     'sbg:x': -331.452392578125
     'sbg:y': 23.596216201782227
@@ -206,7 +206,7 @@ steps:
     out:
       - id: sourcedb
       - id: log
-    run: ../steps/makesourcedb.cwl
+    run: ../lofar-cwl/steps/makesourcedb.cwl
     label: make_sourcedb_ateam
     'sbg:x': -628.7400512695312
     'sbg:y': -847.117919921875

workflows/prefactor_calibrator_test.cwl

@@ -129,7 +129,7 @@ steps:
     out:
       - id: output_imag
       - id: logfile
-    run: ../steps/check_ateam_separation.cwl
+    run: ../lofar-cwl/steps/check_ateam_separation.cwl
     label: check_Ateam_separation
     'sbg:x': -331.452392578125
     'sbg:y': 23.596216201782227
@@ -140,7 +140,7 @@ steps:
     out:
       - id: sourcedb
       - id: log
-    run: ../steps/makesourcedb.cwl
+    run: ../lofar-cwl/steps/makesourcedb.cwl
     label: make_sourcedb_ateam
     'sbg:x': -647.0108642578125
     'sbg:y': -981.3153076171875