first workflow structure design

Former-commit-id: 1df2b264

workflows/HBA.cwl

+class: Workflow
+cwlVersion: v1.0
+id: HBA
+label: HBA.cwl
+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
+inputs:
+  - id: msin_calibrator
+    type: 'Directory[]'
+    'sbg:x': -245
+    'sbg:y': -44
+  - id: min_separation_Ateam
+    type: float
+    default: 30
+    'sbg:x': -265
+    'sbg:y': -153
+  - id: filter_baseline
+    type: string
+    default: '*&'
+    'sbg:x': 145
+    'sbg:y': 85
+  - id: flag_baselines
+    type: string
+    default: '[]'
+    'sbg:x': 9
+    'sbg:y': 232
+  - id: process_baselines_cal
+    type: string
+    default: '*&'
+    'sbg:x': -320
+    'sbg:y': 220
+  - id: raw_data
+    type: boolean
+    default: false
+    'sbg:x': 258
+    'sbg:y': -49
+  - id: memoryperc
+    type: int
+    default: 90
+    'sbg:x': 206
+    'sbg:y': 212
+  - id: avg_timeresolution
+    type: float
+    default: 4.0
+    'sbg:x': -534
+    'sbg:y': 175
+  - id: avg_freqresolution
+    type: string
+    default: '48.82kHz'
+    'sbg:x': -459
+    'sbg:y': -47
+  - id: demix
+    type: boolean
+    'sbg:x': 255
+    'sbg:y': 96
+  - id: demix_timestep
+    type: int
+    default: 16
+    'sbg:x': 92
+    'sbg:y': 158
+  - id: demix_freqstep
+    type: boolean
+    default: 16
+    'sbg:x': -387
+    'sbg:y': 103
+  - id: demix_target
+    type: string
+    default: ''
+    'sbg:x': -70
+    'sbg:y': 157
+  - id: demix_sources
+    type: string
+    default: '[CasA,CygA]'
+    'sbg:x': -182
+    'sbg:y': 135
+outputs:
+  - id: solutions
+    outputSource:
+      - prefactor/solutions
+    type: File
+    'sbg:x': 99
+    'sbg:y': -44
+steps:
+  - id: prefactor
+    in:
+      - id: msin
+        source:
+          - msin_calibrator
+    out:
+      - id: solutions
+    run: ./prefactor.cwl
+    label: prefactor.cwl
+    'sbg:x': -72.39886474609375
+    'sbg:y': -44.5
+requirements:
+  - class: SubworkflowFeatureRequirement

workflows/prefactor.cwl

+class: Workflow
+cwlVersion: v1.0
+id: prefactor
+label: prefactor.cwl
+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
+inputs:
+  - id: msin
+    type: 'Directory[]'
+    'sbg:x': -708.0858764648438
+    'sbg:y': -306
+outputs:
+  - id: solutions
+    outputSource:
+      - prefactor_target/solutions
+    type: File
+    'sbg:x': -169.21875
+    'sbg:y': -319.5
+steps:
+  - id: prefactor_target
+    in:
+      - id: cal_solutions
+        source: prefactor_calibrator/outh5parm
+    out:
+      - id: solutions
+    run: ./prefactor_target.cwl
+    label: prefactor_target
+    'sbg:x': -345
+    'sbg:y': -321
+  - id: prefactor_calibrator
+    in:
+      - id: msin
+        source:
+          - msin
+    out:
+      - id: outh5parm
+    run: ./prefactor_calibrator.cwl
+    label: prefactor_calibrator
+    'sbg:x': -520
+    'sbg:y': -324
+requirements:
+  - class: SubworkflowFeatureRequirement

workflows/prefactor_calibrator.cwl

@@ -22,16 +22,6 @@ inputs:
     'sbg:x': -175.89886474609375
     'sbg:y': -724.5
 outputs:
-  - id: demix_parmdb
-    outputSource:
-      - ndppp_prep_cal/demix_parmdb
-    type:
-      - 'null'
-      - Directory
-      - type: array
-        items: Directory
-    'sbg:x': -67.85011291503906
-    'sbg:y': -356.76287841796875
   - id: outh5parm
     outputSource:
       - h5parm_collector/outh5parm
@@ -60,7 +50,7 @@ steps:
     out:
       - id: msout
       - id: demix_parmdb
-    run: subworkflow/ndppp_prep_cal.cwl
+    run: ../subworkflow/ndppp_prep_cal.cwl
     label: ndppp_prep_cal
     scatter:
       - msin
@@ -73,7 +63,7 @@ steps:
           - ndppp_prep_cal/msout
     out:
       - id: output_ms
-    run: steps/AOFlagger.cwl
+    run: ../steps/AOFlagger.cwl
     label: AOFlagger
     scatterMethod: flat_crossproduct
     'sbg:x': -164
@@ -87,7 +77,7 @@ steps:
     out:
       - id: h5parm
       - id: msout
-    run: subworkflow/calib_cal.cwl
+    run: ../subworkflow/calib_cal.cwl
     label: calib_cal
     scatter:
       - msin
@@ -100,7 +90,7 @@ steps:
           - calib_cal/h5parm
     out:
       - id: outh5parm
-    run: steps/H5ParmCollector.cwl
+    run: ../steps/H5ParmCollector.cwl
     label: H5parm_collector
     'sbg:x': 292.1979675292969
     'sbg:y': -543.7208251953125

workflows/prefactor_target.cwl

+class: Workflow
+cwlVersion: v1.0
+id: prefactor_target
+label: prefactor_target
+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
+inputs:
+  - id: cal_solutions
+    type: File
+    'sbg:x': -327
+    'sbg:y': -42
+outputs:
+  - id: solutions
+    outputSource:
+      - cal_solutions
+    type: File
+    'sbg:x': -58
+    'sbg:y': -43
+    source: input.cal_solutions
+steps: []
+requirements: []