diff --git a/workflows/scRNAseq/velocyto/CHANGELOG.md b/workflows/scRNAseq/velocyto/CHANGELOG.md
index cb2f3df802..b76a496f4d 100644
--- a/workflows/scRNAseq/velocyto/CHANGELOG.md
+++ b/workflows/scRNAseq/velocyto/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.3] - 2025-10-08
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/velocyto_cli/velocyto_cli/0.17.17+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/velocyto_cli/velocyto_cli/0.17.17+galaxy3`
+
 ## [0.2] - 2024-02-05
 
 ### Automatic update
diff --git a/workflows/scRNAseq/velocyto/Velocyto-on10X-filtered-barcodes.ga b/workflows/scRNAseq/velocyto/Velocyto-on10X-filtered-barcodes.ga
index d86c39afa3..067409c70a 100644
--- a/workflows/scRNAseq/velocyto/Velocyto-on10X-filtered-barcodes.ga
+++ b/workflows/scRNAseq/velocyto/Velocyto-on10X-filtered-barcodes.ga
@@ -11,7 +11,6 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.2",
     "name": "RNA Velocity Analysis: Velocyto for 10X Data with Filtered Barcodes",
     "steps": {
         "0": {
@@ -34,7 +33,7 @@
                 "top": 0
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"tag\": \"\", \"collection_type\": \"list\"}",
+            "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"tag\": \"\", \"collection_type\": \"list\", \"fields\": null}",
             "tool_version": null,
             "type": "data_collection_input",
             "uuid": "043d198b-3af0-477d-be11-5d1373280379",
@@ -61,7 +60,7 @@
                 "top": 108.33333333333333
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"format\": [\"tsv\"], \"tag\": \"\", \"collection_type\": \"list\"}",
+            "tool_state": "{\"optional\": false, \"format\": [\"tsv\"], \"tag\": \"\", \"collection_type\": \"list\", \"fields\": null}",
             "tool_version": null,
             "type": "data_collection_input",
             "uuid": "03b0d22c-3b46-4460-8c18-b524bc09d655",
@@ -97,7 +96,7 @@
         },
         "3": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/velocyto_cli/velocyto_cli/0.17.17+galaxy2",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/velocyto_cli/velocyto_cli/0.17.17+galaxy3",
             "errors": null,
             "id": 3,
             "input_connections": {
@@ -149,15 +148,15 @@
                 "top": 116.32222493489576
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/velocyto_cli/velocyto_cli/0.17.17+galaxy2",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/velocyto_cli/velocyto_cli/0.17.17+galaxy3",
             "tool_shed_repository": {
-                "changeset_revision": "90e95e9ee190",
+                "changeset_revision": "f66590d0d3af",
                 "name": "velocyto_cli",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"main\": {\"do\": \"run10x\", \"__current_case__\": 0, \"sample_definition\": {\"sample_definition_select\": \"identifier\", \"__current_case__\": 1}, \"BAM\": {\"__class__\": \"ConnectedValue\"}, \"barcodes\": {\"__class__\": \"ConnectedValue\"}, \"gtffile\": {\"__class__\": \"ConnectedValue\"}, \"s\": {\"__class__\": \"RuntimeValue\"}, \"m\": {\"__class__\": \"RuntimeValue\"}, \"M\": false, \"t\": \"uint16\"}, \"verbosity\": \"-vv\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "0.17.17+galaxy2",
+            "tool_version": "0.17.17+galaxy3",
             "type": "tool",
             "uuid": "f9aef50f-b31d-44dd-aad6-fe4d520e3b1e",
             "when": null,
@@ -173,6 +172,7 @@
     "tags": [
         "name:single-cell"
     ],
-    "uuid": "33862923-af05-48ba-aec5-14393981cee2",
-    "version": 4
+    "uuid": "48e85fa5-62d9-4fbb-8111-e2344360e882",
+    "version": 1,
+    "release": "0.3"
 }
\ No newline at end of file
diff --git a/workflows/scRNAseq/velocyto/Velocyto-on10X-from-bundled.ga b/workflows/scRNAseq/velocyto/Velocyto-on10X-from-bundled.ga
index 07a77e9f49..f9d00cfd48 100644
--- a/workflows/scRNAseq/velocyto/Velocyto-on10X-from-bundled.ga
+++ b/workflows/scRNAseq/velocyto/Velocyto-on10X-from-bundled.ga
@@ -11,7 +11,6 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.2",
     "name": "RNA Velocity Analysis: Velocyto for 10X Data from Bundled Output",
     "steps": {
         "0": {
@@ -34,7 +33,7 @@
                 "top": 0
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"tag\": \"\", \"collection_type\": \"list\"}",
+            "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"tag\": \"\", \"collection_type\": \"list\", \"fields\": null}",
             "tool_version": null,
             "type": "data_collection_input",
             "uuid": "043d198b-3af0-477d-be11-5d1373280379",
@@ -61,7 +60,7 @@
                 "top": 139
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}",
+            "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\", \"fields\": null}",
             "tool_version": null,
             "type": "data_collection_input",
             "uuid": "03b0d22c-3b46-4460-8c18-b524bc09d655",
@@ -106,12 +105,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Apply rules",
-                    "name": "input"
-                }
-            ],
+            "inputs": [],
             "label": "extract barcodes from bundle",
             "name": "Apply rules",
             "outputs": [
@@ -202,7 +196,7 @@
                             "top": 0.0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"tag\": \"\", \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"tag\": \"\", \"collection_type\": \"list\", \"fields\": null}",
                         "tool_version": null,
                         "type": "data_collection_input",
                         "uuid": "043d198b-3af0-477d-be11-5d1373280379",
@@ -229,7 +223,7 @@
                             "top": 108.33333333333333
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"tsv\"], \"tag\": \"\", \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"tsv\"], \"tag\": \"\", \"collection_type\": \"list\", \"fields\": null}",
                         "tool_version": null,
                         "type": "data_collection_input",
                         "uuid": "03b0d22c-3b46-4460-8c18-b524bc09d655",
@@ -265,7 +259,7 @@
                     },
                     "3": {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/velocyto_cli/velocyto_cli/0.17.17+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/velocyto_cli/velocyto_cli/0.17.17+galaxy3",
                         "errors": null,
                         "id": 3,
                         "input_connections": {
@@ -317,15 +311,15 @@
                             "top": 116.32222493489576
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/velocyto_cli/velocyto_cli/0.17.17+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/velocyto_cli/velocyto_cli/0.17.17+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "90e95e9ee190",
+                            "changeset_revision": "f66590d0d3af",
                             "name": "velocyto_cli",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
                         "tool_state": "{\"main\": {\"do\": \"run10x\", \"__current_case__\": 0, \"sample_definition\": {\"sample_definition_select\": \"identifier\", \"__current_case__\": 1}, \"BAM\": {\"__class__\": \"ConnectedValue\"}, \"barcodes\": {\"__class__\": \"ConnectedValue\"}, \"gtffile\": {\"__class__\": \"ConnectedValue\"}, \"s\": {\"__class__\": \"RuntimeValue\"}, \"m\": {\"__class__\": \"RuntimeValue\"}, \"M\": false, \"t\": \"uint16\"}, \"verbosity\": \"-vv\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.17.17+galaxy2",
+                        "tool_version": "0.17.17+galaxy3",
                         "type": "tool",
                         "uuid": "f9aef50f-b31d-44dd-aad6-fe4d520e3b1e",
                         "when": null,
@@ -338,8 +332,8 @@
                         ]
                     }
                 },
-                "tags": "",
-                "uuid": "66e3b8eb-d312-488e-b407-1ed3fa627ebb"
+                "tags": [],
+                "uuid": "706bae3e-e38f-402f-acaa-d2e9f43a18e9"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -357,6 +351,7 @@
     "tags": [
         "name:single-cell"
     ],
-    "uuid": "0608c7f4-767c-47b3-ae45-4e98c7c83bec",
-    "version": 8
+    "uuid": "713dc9d4-d0c0-4bb0-9a55-ee1767515690",
+    "version": 1,
+    "release": "0.3"
 }
\ No newline at end of file