diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga
index 01f528a620..870cb0f4d3 100644
--- a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga
+++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga
@@ -506,7 +506,12 @@
                                 "output_name": "integer_param"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Map parameter value",
+                                "name": "input_param_type"
+                            }
+                        ],
                         "label": null,
                         "name": "Map parameter value",
                         "outputs": [
@@ -901,7 +906,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "33defbd1-e74b-4902-8d84-abe335908dad"
+                "uuid": "48372b98-5e8e-4a3e-923b-a2bda608cc75"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -930,7 +935,16 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool NCBI FCS GX",
+                    "name": "mode"
+                },
+                {
+                    "description": "runtime parameter for tool NCBI FCS GX",
+                    "name": "mode"
+                }
+            ],
             "label": null,
             "name": "NCBI FCS GX",
             "outputs": [
@@ -985,7 +999,12 @@
                     "output_name": "clean_fasta"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool NCBI BLAST+ dustmasker",
+                    "name": "db_opts"
+                }
+            ],
             "label": "soft-masking ",
             "name": "NCBI BLAST+ dustmasker",
             "outputs": [
@@ -1087,7 +1106,20 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool NCBI FCS GX",
+                    "name": "mode"
+                },
+                {
+                    "description": "runtime parameter for tool NCBI FCS GX",
+                    "name": "mode"
+                },
+                {
+                    "description": "runtime parameter for tool NCBI FCS GX",
+                    "name": "mode"
+                }
+            ],
             "label": null,
             "name": "NCBI FCS GX",
             "outputs": [
@@ -1214,7 +1246,16 @@
                     "output_name": "outfile"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool NCBI FCS GX",
+                    "name": "mode"
+                },
+                {
+                    "description": "runtime parameter for tool NCBI FCS GX",
+                    "name": "mode"
+                }
+            ],
             "label": null,
             "name": "NCBI FCS GX",
             "outputs": [
@@ -1368,7 +1409,7 @@
         },
         "18": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2",
             "errors": null,
             "id": 18,
             "input_connections": {
@@ -1381,7 +1422,20 @@
                     "output_name": "mito_scaff_names"
                 }
             },
-            "inputs": [],
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool gfastats",
+                    "name": "mode_condition"
+                },
+                {
+                    "description": "runtime parameter for tool gfastats",
+                    "name": "target_condition"
+                },
+                {
+                    "description": "runtime parameter for tool gfastats",
+                    "name": "target_condition"
+                }
+            ],
             "label": "removing scaffolds ",
             "name": "gfastats",
             "outputs": [
@@ -1403,16 +1457,16 @@
                     "output_name": "output"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2",
             "tool_shed_repository": {
-                "changeset_revision": "0fe699ced54f",
+                "changeset_revision": "10dc0f5a82e2",
                 "name": "gfastats",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"sort\": \"\", \"remove_terminal_gaps\": true, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"RuntimeValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"RuntimeValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"sort\": \"\", \"remove_terminal_gaps\": true, \"homopolymer_compress\": null, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"RuntimeValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
-            "tool_version": "1.3.11+galaxy1",
+            "tool_version": "1.3.11+galaxy2",
             "type": "tool",
             "uuid": "5113c945-c811-4cbc-81ac-20d1d80e97ed",
             "when": null,
@@ -1428,7 +1482,7 @@
     "tags": [
         "VGP_curated"
     ],
-    "uuid": "afdeece1-bd77-47b6-be22-c284135bf80c",
+    "uuid": "2a7adfc0-3bbf-4c61-8226-d8180445331d",
     "version": 1,
-    "release": "1.3"
-}
+    "release": "1.4"
+}
\ No newline at end of file
diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md
index 4694ce36e9..512f067279 100644
--- a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md
+++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [1.4] - 2026-03-16
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy2`
+
 ## [1.3] - 2026-01-26
 
 ### Automatic update