Add demo imaging pipeline

prefactor_calibrator_image.cwl

+class: Workflow
+cwlVersion: v1.0
+id: prefactor_calibrator_image
+label: prefactor_calibrator_image
+$namespaces:
+  sbg: 'https://www.sevenbridges.com/'
+inputs:
+  - id: msin
+    type: 'Directory[]'
+    'sbg:x': -549
+    'sbg:y': -168
+outputs:
+  - id: image
+    outputSource:
+      - wsclean/image
+    type: 'File[]'
+    'sbg:x': 206
+    'sbg:y': -189
+  - id: dirty_image
+    outputSource:
+      - wsclean/dirty_image
+    type: 'File[]'
+    'sbg:x': 271
+    'sbg:y': -87
+  - id: image_1
+    outputSource:
+      - wsclean_1/image
+    type: 'File[]'
+    'sbg:x': -133
+    'sbg:y': -405
+  - id: dirty_image_1
+    outputSource:
+      - wsclean_1/dirty_image
+    type: 'File[]'
+    'sbg:x': -26
+    'sbg:y': -292
+steps:
+  - id: prefactor_calibrator
+    in:
+      - id: msin
+        source:
+          - msin
+      - id: raw_data
+        default: true
+      - id: demix
+        default: false
+    out:
+      - id: demix_parmdb
+      - id: output_ms
+    run: ./prefactor_calibrator.cwl
+    label: prefactor_calibrator
+    'sbg:x': -234
+    'sbg:y': -94
+  - id: wsclean
+    in:
+      - id: image_name
+        source: msin
+        valueFrom: $(inputs.msin.basename)
+      - id: msin
+        source: prefactor_calibrator/output_ms
+    out:
+      - id: dirty_image
+      - id: image
+    run: steps/wsclean.cwl
+    label: WSClean
+    scatter:
+      - msin
+    'sbg:x': 6
+    'sbg:y': -102
+  - id: wsclean_1
+    in:
+      - id: image_name
+        source: msin
+        valueFrom: flagged_$(inputs.msin.basename)
+      - id: msin
+        source: msin
+    out:
+      - id: dirty_image
+      - id: image
+    run: steps/wsclean.cwl
+    label: WSClean
+    scatter:
+      - msin
+    'sbg:x': -317
+    'sbg:y': -302
+requirements:
+  - class: SubworkflowFeatureRequirement
+  - class: ScatterFeatureRequirement
+  - class: StepInputExpressionRequirement
+  - class: InlineJavascriptRequirement

test_jobs/demo_prefactor.json

+{
+    "msin": [
+        {
+            "class": "Directory",
+            "path": "/home/mmancini/git/prefactor3-cwl/test_data/L570745_SB003_uv_first10.MS"
+        },
+        {
+            "class": "Directory",
+            "path": "/home/mmancini/git/prefactor3-cwl/test_data/L570745_SB005_uv_first10.MS"
+        },
+        {
+            "class": "Directory",
+            "path": "/home/mmancini/git/prefactor3-cwl/test_data/L570745_SB008_uv_first10.MS"
+        }
+    ]
+}
+