diff --git a/exec/src/klio_exec/commands/run.py b/exec/src/klio_exec/commands/run.py
index c959a4e3..b7854711 100644
--- a/exec/src/klio_exec/commands/run.py
+++ b/exec/src/klio_exec/commands/run.py
@@ -476,7 +476,7 @@ def _generate_pcoll_per_input(self, pipeline):
         to_process = MultiInputPCollTuple(**input_name_to_input_pcolls)
         to_pass_thru = (
             multi_to_pass_thru
-            | "Merge multi-input pass-thrus" >> beam.Flatten()
+            | "Merge multi-input pass-thrus" >> beam.Flatten(pipeline=pipeline)
         )
         return to_process, to_pass_thru