Add control section for keep_input

download_and_compress_pipeline.cwl

@@ -39,6 +39,10 @@ outputs:
   type: Any
   outputSource:
   - format_quality_metrics/formatted_quality
+- id: control
+  type: Any
+  outputSource:
+  - format_quality_metrics/control
 - id: inspect
   type: File
   outputSource:
@@ -71,7 +75,7 @@ steps:
   - id: inspect
   - id: logfile
   - id: ingest
-  - id: keep_inputs
+  - id: keep_input
   - id: applied_fixes
   - id: unfixable_issues
 - id: combine
@@ -97,8 +101,8 @@ steps:
     source: extract_metrics/quality
   - id: msin
     source: fetch_data/uncompressed
-  - id: keep_inputs
-    source: compress/keep_inputs
+  - id: keep_input
+    source: compress/keep_input
   - id: applied_fixes
     source: compress/applied_fixes
   - id: unfixable_issues
@@ -106,3 +110,4 @@ steps:
   run: steps/format_metrics.cwl
   out:
   - formatted_quality
+  - control

steps/format_metrics.cwl

@@ -15,7 +15,7 @@ inputs:
   type:
     type: array
     items: Directory
-- id: keep_inputs
+- id: keep_input
   type:
     type: array
     items: boolean
@@ -35,19 +35,33 @@ inputs:
 outputs:
 - id: formatted_quality
   type: Any
+- id: control
+  type: Any
+
 expression: |
   ${
 
-    var result = {
+    var quality = {
       'plots': inputs.plots,
       'summary': inputs.quality
     };
-    result['summary']['keep_inputs'] = inputs.msin.map((file, index) => ({
-      name: file.basename,
-      keep: inputs.keep_inputs[index]
-    }));
-    result['summary']['applied_fixes'] = inputs.applied_fixes[0]
-    result['summary']['unfixable_issues'] = inputs.unfixable_issues[0]
-    return {'formatted_quality': result}
 
+    quality['summary']['applied_fixes'] = inputs.applied_fixes[0];
+    quality['summary']['unfixable_issues'] = inputs.unfixable_issues[0];
+
+    var control = {
+      'keep_input': inputs.msin.map((file, index) => {
+        if (inputs.keep_input[index]) {
+          return {
+            surl: file.location
+          };
+        }
+        return null;
+      }).filter(item => item !== null)
+    };
+
+    return {
+      'formatted_quality': quality,
+      'control': control
+    };
   }