From 48aa202835267e8cceebc20da8f4f6663873efe2 Mon Sep 17 00:00:00 2001
From: Yousef Moazzam <yousef.moazzam@diamond.ac.uk>
Date: Fri, 15 May 2026 14:36:20 +0100
Subject: [PATCH] Use copied pipeline file for pipeline input

---
 httomo/cli.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/httomo/cli.py b/httomo/cli.py
index 97f1711b5..8cfd9a3d1 100644
--- a/httomo/cli.py
+++ b/httomo/cli.py
@@ -274,7 +274,15 @@ def run(
         PipelineFormat.Json if pipeline_format == "Json" else PipelineFormat.Yaml
     )
     pipeline_object = generate_pipeline(
-        in_data_file, pipeline, save_all, method_wrapper_comm, format_enum
+        in_data_file,
+        (
+            httomo.globals.run_out_dir / pipeline.name
+            if format_enum == PipelineFormat.Yaml
+            else pipeline
+        ),
+        save_all,
+        method_wrapper_comm,
+        format_enum,
     )
 
     if not does_contain_sweep: