diff --git a/workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/CHANGELOG.md b/workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/CHANGELOG.md
index dfdc1d8925..4b5092c4cd 100644
--- a/workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/CHANGELOG.md
+++ b/workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/CHANGELOG.md
@@ -1,5 +1,12 @@
 # Changelog
 
+## [0.4] - 2026-04-20
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3`
+- `toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/1.2`
+- `toolshed.g2.bx.psu.edu/repos/iuc/kegg_pathways_completeness/kegg_pathways_completeness/1.3.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/kegg_pathways_completeness/kegg_pathways_completeness/1.4.3+galaxy0`
+
 ## [0.3] - 2026-03-27
 
 - Set a parameter from Add toolshed.g2.bx.psu.edu/repos/iuc/kegg_pathways_completeness/kegg_pathways_completeness/1.3.0+galaxy0 to true to have a second and more detailed per contig output
diff --git a/workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/Functional_annotation_of_sequences.ga b/workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/Functional_annotation_of_sequences.ga
index 24a642c24d..3ddbc74e8c 100644
--- a/workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/Functional_annotation_of_sequences.ga
+++ b/workflows/genome_annotation/functional-annotation/functional-annotation-of-sequences/Functional_annotation_of_sequences.ga
@@ -39,7 +39,6 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.3",
     "name": "Functional annotation of sequences",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
@@ -797,7 +796,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "e109aec1-e620-4101-ba74-97c00a7b2159"
+                "uuid": "a5a7dc54-b22a-40ab-b167-b849b85f79d8"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -807,7 +806,7 @@
         },
         "6": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3",
             "errors": null,
             "id": 6,
             "input_connections": {
@@ -838,16 +837,16 @@
                     "output_name": "output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3",
             "tool_shed_repository": {
-                "changeset_revision": "d3c07d270a50",
+                "changeset_revision": "3e27acfa4830",
                 "name": "collection_element_identifiers",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
-            "tool_version": "0.0.2",
+            "tool_version": "0.0.3",
             "type": "tool",
             "uuid": "53019ea6-e2ff-449d-9d21-75425a4bc29c",
             "when": null,
@@ -1210,7 +1209,7 @@
         },
         "15": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kegg_pathways_completeness/kegg_pathways_completeness/1.3.0+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kegg_pathways_completeness/kegg_pathways_completeness/1.4.3+galaxy0",
             "errors": null,
             "id": 15,
             "input_connections": {
@@ -1230,15 +1229,7 @@
                 },
                 {
                     "description": "runtime parameter for tool Calculate KEGG Pathways completeness",
-                    "name": "usr_ref_files"
-                },
-                {
-                    "description": "runtime parameter for tool Calculate KEGG Pathways completeness",
-                    "name": "usr_ref_files"
-                },
-                {
-                    "description": "runtime parameter for tool Calculate KEGG Pathways completeness",
-                    "name": "usr_ref_files"
+                    "name": "t"
                 }
             ],
             "label": null,
@@ -1273,16 +1264,16 @@
                     "output_name": "kegg_pathways_table"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kegg_pathways_completeness/kegg_pathways_completeness/1.3.0+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kegg_pathways_completeness/kegg_pathways_completeness/1.4.3+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "9933e2f91584",
+                "changeset_revision": "78990897aa94",
                 "name": "kegg_pathways_completeness",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"input_type\": {\"select_input_type\": \"input_file\", \"__current_case__\": 0, \"i\": {\"__class__\": \"ConnectedValue\"}, \"m\": true}, \"p\": false, \"usr_ref_files\": {\"definitions\": {\"__class__\": \"RuntimeValue\"}, \"names\": {\"__class__\": \"RuntimeValue\"}, \"classes\": {\"__class__\": \"RuntimeValue\"}}, \"w\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"input_type\": {\"select_input_type\": \"input_file\", \"__current_case__\": 0, \"i\": {\"__class__\": \"ConnectedValue\"}, \"m\": true}, \"p\": false, \"t\": {\"__class__\": \"RuntimeValue\"}, \"usr_ref_files\": {\"classes\": {\"__class__\": \"RuntimeValue\"}, \"definitions\": {\"__class__\": \"RuntimeValue\"}, \"names\": {\"__class__\": \"RuntimeValue\"}}, \"w\": false, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
-            "tool_version": "1.3.0+galaxy0",
+            "tool_version": "1.4.3+galaxy0",
             "type": "tool",
             "uuid": "1dd5a227-60ed-48ca-b5e3-ea3914d3f2b5",
             "when": "$(inputs.when)",
@@ -1301,6 +1292,7 @@
         }
     },
     "tags": [],
-    "uuid": "e1e6ce2d-d7c5-45a6-93eb-d730768f7c06",
-    "version": 1
+    "uuid": "005f5d67-79e0-4385-bbbc-cbc84ef88160",
+    "version": 1,
+    "release": "0.4"
 }
\ No newline at end of file