diff --git a/workflows/transcriptomics/rnaseq-de/CHANGELOG.md b/workflows/transcriptomics/rnaseq-de/CHANGELOG.md
index 5a03ad4284..8f7ce2573a 100644
--- a/workflows/transcriptomics/rnaseq-de/CHANGELOG.md
+++ b/workflows/transcriptomics/rnaseq-de/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.12] - 2026-07-27
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4`
+
 
 ## [0.11] - 2026-07-14
 
diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga
index 69e920f1c4..9f3d8d7707 100644
--- a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga
+++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga
@@ -221,7 +221,7 @@
         },
         "7": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy3",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4",
             "errors": null,
             "id": 7,
             "input_connections": {
@@ -279,16 +279,16 @@
                     "output_name": "deseq_out"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy3",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy4",
             "tool_shed_repository": {
-                "changeset_revision": "b060944b3989",
+                "changeset_revision": "05f9e54d7e81",
                 "name": "deseq2",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"advanced_options\": {\"esf_cond\": {\"esf\": \"\", \"__current_case__\": 0}, \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}, \"use_beta_priors\": false, \"lfc_shrinkage_type\": \"none\"}, \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"header\": {\"__class__\": \"ConnectedValue\"}, \"output_options\": {\"output_selector\": [\"pdf\", \"normCounts\"], \"alpha_ma\": {\"__class__\": \"ConnectedValue\"}}, \"select_data\": {\"how\": \"datasets_per_level\", \"__current_case__\": 1, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": \"DEFactor\", \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": \"MainFactor\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"factorLevel\": \"BaseFactor\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
-            "tool_version": "2.11.40.8+galaxy3",
+            "tool_version": "2.11.40.8+galaxy4",
             "type": "tool",
             "uuid": "45883538-b692-4e35-8dee-d08974682a9c",
             "when": null,
@@ -1062,7 +1062,7 @@
         "transcriptomics",
         "RNAseq"
     ],
-    "uuid": "80a29f89-9cb8-4e9e-b660-9052ce7c21cd",
+    "uuid": "67da5cdb-0027-4901-99b3-9b910e29a4a5",
     "version": 1,
-    "release": "0.11"
-}
+    "release": "0.12"
+}
\ No newline at end of file