Merge branch 'already_compressed_in_output' into 'master'

Put 'already_compressed' in output json if the data was already dysco-compressed

See merge request !5

download_and_compress_pipeline.cwl

@@ -47,6 +47,13 @@ outputs:
   type: File
   outputSource:
   - combine/inspect_file
+- id: input_storage_manager
+  type: string[]
+  outputSource: compress/input_storage_manager
+- id: already_compressed
+  type: boolean[]
+  outputSource: already_compressed/already_compressed
+
 
 steps:
 - id: fetch_data
@@ -78,6 +85,7 @@ steps:
   - id: keep_input
   - id: applied_fixes
   - id: unfixable_issues
+  - id: input_storage_manager
 - id: combine
   in:
   - id: inputs
@@ -111,3 +119,26 @@ steps:
   out:
   - formatted_quality
   - control
+
+- id: already_compressed
+  run:
+    class: ExpressionTool
+    requirements:
+      - class: InlineJavascriptRequirement
+    inputs:
+      - id: input_storage_manager
+        type: string[]
+    outputs:
+      - id: already_compressed
+        type: boolean[]
+    expression: |
+      ${
+        return {
+          already_compressed: inputs.input_storage_manager == "DyscoStorageManager"
+        };
+      }
+  in:
+    - id: input_storage_manager
+      source: compress/input_storage_manager
+  out:
+    - id: already_compressed
\ No newline at end of file