add concat_ms

Former-commit-id: b8393300

lofar-cwl/steps/ms_concat.cwl

@@ -3,14 +3,13 @@ cwlVersion: v1.0
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: ms_concat
-
-
 baseCommand:
-  - concat_MS.py
+  - python3
+  - /usr/local/bin/concat_MS_CWL.py
 inputs:
-  - id: min_length
+  - default: 50
+    id: min_length
     type: int?
-    default: 50
     inputBinding:
       position: 0
       prefix: '--min_length'
@@ -35,25 +34,25 @@ inputs:
       position: 2
 outputs:
   - id: concat_meta_ms
-    type: Directory[]
+    type: 'Directory[]'
     outputBinding:
-      glob: >
+      glob: |
         $(inputs.msout)_[0-9*]
   - id: concat_additional_ms
-    type: Directory[]
+    type: 'Directory[]'
     outputBinding:
       glob: $(inputs.msout)_*_CONCAT
   - id: ms_outs
-    type: Directory[]
+    type: 'Directory[]'
     outputBinding:
       outputEval: $(inputs.msin)
 label: ms_concat
 requirements:
   - class: ShellCommandRequirement
   - class: DockerRequirement
-    dockerPull: lofareosc/lofar-pipeline-ci:latest
-  - class: InlineJavascriptRequirement
+    dockerPull: 'lofareosc/prefactor:HBAcalibrator'
   - class: InitialWorkDirRequirement
     listing:
       - entry: $(inputs.msin)
         writable: true
+  - class: InlineJavascriptRequirement

workflows/prefactor_calibrator.cwl

@@ -266,6 +266,10 @@ steps:
         source: do_smooth
       - id: max_separation_arcmin
         source: max_separation_arcmin
+      - id: min_length
+        source: min_length
+      - id: overhead
+        source: overhead
       - id: min_separation
         source: min_separation
       - id: A-Team_skymodel

workflows/prefactor_calibrator/prep.cwl

@@ -66,32 +66,40 @@ inputs:
     type: boolean
     'sbg:x': -1000
     'sbg:y': 500
-  - id: min_separation
+  - id: min_length
     type: int?
     'sbg:x': -1000
     'sbg:y': 600
-  - id: max_separation_arcmin
+  - id: overhead
     type: float?
     'sbg:x': -1000
     'sbg:y': 700
+  - id: min_separation
+    type: int?
+    'sbg:x': -1000
+    'sbg:y': 800
+  - id: max_separation_arcmin
+    type: float?
+    'sbg:x': -1000
+    'sbg:y': 900
   - id: calibrator_path_skymodel
     type: Directory?
     'sbg:x': -1000
-    'sbg:y': 800
+    'sbg:y': 1000
   - id: A-Team_skymodel
     type: File?
     'sbg:x': -1000
-    'sbg:y': 900
+    'sbg:y': 1100
   - id: elevation
     type: string
     default: 0deg..20deg
     'sbg:x': -1000
-    'sbg:y': 1000
+    'sbg:y': 1200
   - id: amplmin
     type: float
     default: 1.e-30
     'sbg:x': -1000
-    'sbg:y': 1100
+    'sbg:y': 1300
 outputs:
   - id: check_Ateam_separation.png
     outputSource:
@@ -113,7 +121,7 @@ outputs:
     'sbg:y': -100
   - id: msout
     outputSource:
-      - ndppp_prep_cal/msout
+      - ms_concat/ms_outs
     type: 'Directory[]'
     'sbg:x': 1000
     'sbg:y': 0
@@ -225,18 +233,37 @@ steps:
   - id: find_skymodel_cal
     in:
       - id: msin
-        source: msin
+        source:
+          - msin
       - id: skymodels
         source: calibrator_path_skymodel
       - id: max_separation_arcmin
         source: max_separation_arcmin
     out:
       - id: output_models
+      - id: model_name
       - id: logfile
     run: ../../steps/find_skymodel_cal.cwl
     label: find_skymodel_cal
     'sbg:x': -500
     'sbg:y': 500
+  - id: ms_concat
+    in:
+      - id: min_length
+        source: min_length
+      - id: overhead
+        source: overhead
+      - id: msin
+        source:
+          - ndppp_prep_cal/msout
+    out:
+      - id: concat_meta_ms
+      - id: concat_additional_ms
+      - id: ms_outs
+    run: ../../lofar-cwl/steps/ms_concat.cwl
+    label: ms_concat
+    'sbg:x': 300
+    'sbg:y': 0
 requirements:
   - class: SubworkflowFeatureRequirement
   - class: ScatterFeatureRequirement