keep_input summary now for each scattered msin

download_and_compress_pipeline.cwl

@@ -95,6 +95,8 @@ steps:
     source: extract_metrics/plots
   - id: quality
     source: extract_metrics/quality
+  - id: msin
+    source: fetch_data/uncompressed
   - id: keep_inputs
     source: compress/keep_inputs
   - id: applied_fixes

steps/format_metrics.cwl

@@ -11,6 +11,10 @@ inputs:
   type: File[]
 - id: quality
   type: Any
+- id: msin
+  type:
+    type: array
+    items: Directory
 - id: keep_inputs
   type:
     type: array
@@ -38,7 +42,10 @@ expression: |
               'plots': inputs.plots,
               'summary': inputs.quality
     };
-    result['summary']['keep_inputs'] = inputs.keep_inputs[0]
+    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}