diff --git a/workflows/genome-assembly/assembly-with-flye/CHANGELOG.md b/workflows/genome-assembly/assembly-with-flye/CHANGELOG.md
index 017fa805b2..b854bfdf19 100644
--- a/workflows/genome-assembly/assembly-with-flye/CHANGELOG.md
+++ b/workflows/genome-assembly/assembly-with-flye/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.4] - 2025-10-06
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1`
+
 ## [0.3] - 2025-05-19
 
 ### Automatic update
diff --git a/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye.ga b/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye.ga
index 999ffe7e01..e101668061 100644
--- a/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye.ga
+++ b/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye.ga
@@ -125,7 +125,7 @@
         },
         "2": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1",
             "errors": null,
             "id": 2,
             "input_connections": {
@@ -148,15 +148,15 @@
                 "top": 0
             },
             "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "a3b35edea53a",
+                "changeset_revision": "1b1cf0c96501",
                 "name": "quast",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"al\": {\"ambiguity_score\": \"0.99\", \"ambiguity_usage\": \"one\", \"fragmented\": false, \"fragmented_max_indent\": \"50\", \"min_alignment\": \"65\", \"min_identity\": \"95.0\", \"upper_bound_assembly\": false, \"upper_bound_min_con\": \"2\", \"use_all_alignments\": false}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"circos\": \"false\", \"contig_thresholds\": \"0,1000\", \"extensive_mis_size\": \"1000\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"in\": {\"__current_case__\": 1, \"custom\": \"false\", \"inputs\": {\"__class__\": \"RuntimeValue\"}}, \"k_mer\": {\"__current_case__\": 1, \"k_mer_stats\": \"\"}, \"large\": true, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"scaffold_gap_max_size\": \"1000\", \"skip_unaligned_mis_contigs\": \"false\", \"split_scaffolds\": false, \"strict_NA\": \"false\", \"unaligned_part_size\": \"500\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "5.3.0+galaxy0",
+            "tool_version": "5.3.0+galaxy1",
             "type": "tool",
             "uuid": "5bc29646-ec4c-4eb3-af01-73d82fc690a2",
             "when": null,
@@ -260,7 +260,7 @@
         }
     },
     "tags": [],
-    "uuid": "21643946-a984-4a3f-be71-d480590522c3",
+    "uuid": "a931e57c-44bb-4396-85aa-aa9ac19ff51b",
     "version": 1,
-    "release": "0.3"
+    "release": "0.4"
 }
\ No newline at end of file