diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index 803febfce5c..b6145c1110a 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -1,5 +1,6 @@
 import logging
 import uuid
+from typing import List, Union
 
 from galaxy import model
 from galaxy.util import ExecutionTimer
@@ -270,19 +271,27 @@ class WorkflowProgress:
         return remaining_steps
 
     def replacement_for_input(self, step, input_dict):
-        replacement = modules.NO_REPLACEMENT
+        replacement: Union[
+            modules.NoReplacement,
+            model.DatasetCollectionInstance,
+            List[model.DatasetCollectionInstance],
+        ] = modules.NO_REPLACEMENT
         prefixed_name = input_dict["name"]
         multiple = input_dict["multiple"]
         if prefixed_name in step.input_connections_by_name:
             connection = step.input_connections_by_name[prefixed_name]
             if input_dict["input_type"] == "dataset" and multiple:
-                replacement = [self.replacement_for_connection(c) for c in connection]
+                temp = [self.replacement_for_connection(c) for c in connection]
                 # If replacement is just one dataset collection, replace tool
                 # input_dict with dataset collection - tool framework will extract
                 # datasets properly.
-                if len(replacement) == 1:
-                    if isinstance(replacement[0], model.HistoryDatasetCollectionAssociation):
-                        replacement = replacement[0]
+                if len(temp) == 1:
+                    if isinstance(temp[0], model.HistoryDatasetCollectionAssociation):
+                        replacement = temp[0]
+                    else:
+                        replacement = temp
+                else:
+                    replacement = temp
             else:
                 is_data = input_dict["input_type"] in ["dataset", "dataset_collection"]
                 replacement = self.replacement_for_connection(connection[0], is_data=is_data)
@@ -327,7 +336,7 @@ class WorkflowProgress:
                 if not replacement.is_ok:
                     raise modules.CancelWorkflowEvaluation()
             else:
-                if not replacement.collection.populated:
+                if not replacement.collection.populated:  # type: ignore
                     raise modules.DelayedWorkflowEvaluation()
                 pending = False
                 for dataset_instance in replacement.dataset_instances:
diff --git a/setup.cfg b/setup.cfg
index e30be627080..5161894188d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -602,8 +602,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.main]
 check_untyped_defs = False
-[mypy-galaxy.workflow.run]
-check_untyped_defs = False
 [mypy-galaxy.web.framework.middleware.sqldebug]
 check_untyped_defs = False
 [mypy-galaxy.tools.recommendations]