Merge branch 'unflagged_check' into 'master'

Check for all MS files removed

See merge request eosc/prefactor3-cwl!39

steps/check_filtered_MS_array.cwl

+id: check_filtered_MS_array
+label: check_filtered_MS_array
+class: ExpressionTool
+
+cwlVersion: v1.1
+inputs:
+    - id: input
+      type: Directory[]
+
+outputs:
+    - id: output
+      type: Directory[]
+
+expression: |
+  ${
+    if (inputs.input.length == 0) {
+        throw new Error("No MS files meet the minimum unflagged fraction set by min_unflagged_fraction")
+    } else {
+        return {'output': inputs.input}
+    }
+  }
+
+
+requirements:
+  - class: InlineJavascriptRequirement

workflows/prefactor_target/gsmcal.cwl

@@ -463,10 +463,18 @@ steps:
     label: merge_array_files
     'sbg:x': 1000
     'sbg:y': 100
+  - id: check_filtered_MS_array
+    in:
+      - id: input
+        source: merge_array/output
+    out:
+      - id: output
+    run: ../../steps/check_filtered_MS_array.cwl
+    label: check_filtered_MS_array
   - id: calibrate_target
     in:
       - id: msin
-        source: merge_array/output
+        source: check_filtered_MS_array/output
       - id: skymodel
         source: make_sourcedb_target/sourcedb
       - id: do_smooth