From 2e02f002e338899a0b980ce6f84b62c1dfcbe80b Mon Sep 17 00:00:00 2001
From: Timo Millenaar <tmillenaar@gmail.com>
Date: Fri, 19 Jul 2024 13:06:41 +0200
Subject: [PATCH] Put 'already_compressed' in output json if the data was
 already dysco-compressed

---
 download_and_compress_pipeline.cwl | 31 ++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/download_and_compress_pipeline.cwl b/download_and_compress_pipeline.cwl
index 4eaa444..9a40513 100644
--- a/download_and_compress_pipeline.cwl
+++ b/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
-- 
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