Write results to cwl.output.json to bypass size restrictions

This MR modifies the way LINC collects the output in the filter_ms_group step. The output is written to cwl.output.json, which is then parsed as part of the collection of the outputs. This the loadContents field to circumvent size restrictions.

Solves #63 (closed).

steps/filter_ms_group.cwl

@@ -21,19 +21,16 @@ outputs:
   - id: output
     type: Directory[]
     outputBinding:
-      loadContents: true
-      glob: 'selected_ms.json'
-      outputEval: '$(JSON.parse(self[0].contents))'
+      glob: $(runtime.outdir)/cwl.output.json
+      outputEval: $(self.output)
   - id: selected_ms
     type: string[]
     outputBinding:
-        loadContents: true
-        glob: 'out.json'
-        outputEval: $(JSON.parse(self[0].contents).selected_ms)
+        glob: $(runtime.outdir)/cwl.output.json
+        outputEval: $(self.selected_ms)
 label: filter_ms_group
 
 requirements:
-  - class: InlineJavascriptRequirement
   - class: InitialWorkDirRequirement
     listing:
      - entryname: filter_ms_group.py
@@ -50,23 +47,18 @@ requirements:
         ms_by_name = { ms.split(os.path.sep)[-1]:
                        {'class':'Directory', 'path': ms} for ms in ms_list}
 
-        output_file = 'selected_ms.json'
-
         with open(json_file, 'r') as f_stream:
             selected_ms = json.load(f_stream)[group_id]
 
         selected_ms = [os.path.basename(ms_name) for ms_name in selected_ms]
-        cwl_output  = {'selected_ms': selected_ms}
+        selected_ms_names = [ms_by_name[ms_name] for ms_name in selected_ms
+                                                    if ms_name != 'dummy.ms']
+        cwl_output  = {'selected_ms': selected_ms,
+                       'output': selected_ms_names}
 
-        with open('./out.json', 'w') as fp:
+        with open('./cwl.output.json', 'w') as fp:
             json.dump(cwl_output, fp)
 
-        selected_ms = [ms_by_name[ms_name] for ms_name in selected_ms if ms_name != 'dummy.ms']
-
-
-        with open(output_file, 'w') as f_stream:
-            json.dump(selected_ms, f_stream)
-
 hints:
   - class: InitialWorkDirRequirement
     listing: