Put keep_inputs in summary based on skip_compress

compress_pipeline.cwl

@@ -42,6 +42,9 @@ outputs:
   type: string[]
   outputSource:
   - identify_issues/unfixable_issues
+- id: keep_inputs
+  type: boolean
+  outputSource: identify_issues/skip_compress
 
 steps:
 - id: identify_issues

download_and_compress_pipeline.cwl

@@ -71,6 +71,7 @@ steps:
   - id: inspect
   - id: logfile
   - id: ingest
+  - id: keep_inputs
   - id: applied_fixes
   - id: unfixable_issues
 - id: combine
@@ -94,6 +95,8 @@ steps:
     source: extract_metrics/plots
   - id: quality
     source: extract_metrics/quality
+  - id: keep_inputs
+    source: compress/keep_inputs
   - id: applied_fixes
     source: compress/applied_fixes
   - id: unfixable_issues

steps/format_metrics.cwl

@@ -11,6 +11,10 @@ inputs:
   type: File[]
 - id: quality
   type: Any
+- id: keep_inputs
+  type:
+    type: array
+    items: boolean
 - id: applied_fixes
   type:
     type: array
@@ -34,6 +38,7 @@ expression: |
               'plots': inputs.plots,
               'summary': inputs.quality
     };
+    result['summary']['keep_inputs'] = inputs.keep_inputs[0]
     result['summary']['applied_fixes'] = inputs.applied_fixes[0]
     result['summary']['unfixable_issues'] = inputs.unfixable_issues[0]
     return {'formatted_quality': result}