diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9-tests.yml b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9-tests.yml
index 84faabea1..9ad050ede 100644
--- a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9-tests.yml
+++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9-tests.yml
@@ -9,7 +9,7 @@
     mito_scaff_names:
       asserts:
         has_text: 
-          text: "SCAFFOLD_82"
+          text: "scaffold_82"
     final decontaminated assembly:
       decompress: true
       asserts:
@@ -18,4 +18,4 @@
     contaminants_table:
       asserts:
         has_text: 
-          text: "SCAFFOLD_200"
+          text: "scaffold_200"
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 becfb8caa..4e2cbc599 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
@@ -11,7 +11,7 @@
     ],
     "format-version": "0.1",
     "license": "BSD-3-Clause",
-    "release": "0.2",
+    "release": "0.3",
     "name": "Assembly-decontamination-VGP9",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n### Worflow ran on: \n\n```galaxy\ninvocation_time()\n```\n\n# List of contaminants\n\n\r\n```galaxy\nhistory_dataset_as_table(output=\"contaminants_table\")\n```\r\n\n\n# List of Mitochondrial scaffolds\n\r\n```galaxy\nhistory_dataset_as_table(output=\"mito_scaff_names\")\n```\r\n\n\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
@@ -33,8 +33,8 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
-                "left": 0,
-                "top": 579.578125
+                "left": 0.0,
+                "top": 573.2100224386197
             },
             "tool_id": null,
             "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}",
@@ -60,7 +60,7 @@
             "name": "Input parameter",
             "outputs": [],
             "position": {
-                "left": 72.984375,
+                "left": 0.5475811709443406,
                 "top": 692.7734375
             },
             "tool_id": null,
@@ -73,70 +73,18 @@
                 {
                     "label": null,
                     "output_name": "output",
-                    "uuid": "9b1c5517-60c3-49b5-9e9e-f85e883b6a5f"
+                    "uuid": "34f0edb5-742e-4de2-923f-1fb93e511ca9"
                 }
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-            "inputs": [],
-            "label": "lower to uppercase",
-            "name": "Text transformation",
-            "outputs": [
-                {
-                    "name": "output",
-                    "type": "input"
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-            "position": {
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-                "top": 375.78555810947694
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-                "owner": "bgruening",
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-            "tool_version": "9.3+galaxy1",
-            "type": "tool",
-            "uuid": "b9b3d9b9-1716-486d-b65c-b0fb196cbc01",
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-            "workflow_outputs": []
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             "annotation": "",
             "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2",
             "errors": null,
-            "id": 3,
+            "id": 2,
             "input_connections": {
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+                    "id": 0,
                     "output_name": "output"
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             },
@@ -150,8 +98,8 @@
                 }
             ],
             "position": {
-                "left": 652.953125,
-                "top": 323.6484375
+                "left": 463.79758117094434,
+                "top": 292.69140625
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                 "HideDatasetActionoutfile": {
@@ -174,14 +122,14 @@
             "when": null,
             "workflow_outputs": []
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-        "4": {
+        "3": {
             "annotation": "",
             "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
             "errors": null,
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@@ -195,8 +143,8 @@
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             "position": {
-                "left": 972.0000745777726,
-                "top": 355.5823870316441
+                "left": 827.4147686709443,
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@@ -214,30 +162,30 @@
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+            "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"/^>/!y/atcgn/NNNNN/\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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             "uuid": "5089350b-c1a9-498a-9786-9864d484f77a",
             "when": null,
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+            "id": 4,
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                 "single_paired|input_sequences": {
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+                    "id": 3,
                     "output_name": "output"
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             },
@@ -259,7 +207,7 @@
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             ],
             "position": {
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+                "left": 1300.1257061709443,
                 "top": 147.58203125
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@@ -289,14 +237,14 @@
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             "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2",
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+            "id": 5,
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@@ -310,7 +258,7 @@
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             "position": {
-                "left": 1365.8984375,
+                "left": 1293.4616436709443,
                 "top": 539.6171875
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             "post_job_actions": {},
@@ -328,14 +276,14 @@
             "when": null,
             "workflow_outputs": []
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+        "6": {
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             "content_id": "Cut1",
             "errors": null,
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+            "id": 6,
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@@ -349,7 +297,7 @@
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             ],
             "position": {
-                "left": 1727.19921875,
+                "left": 1654.7624249209443,
                 "top": 53.078125
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@@ -367,59 +315,14 @@
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-                    "output_name": "classified_out_s"
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-            "inputs": [],
-            "label": "contaminant scaffolds",
-            "name": "Search in textfiles",
-            "outputs": [
-                {
-                    "name": "output",
-                    "type": "input"
-                }
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-            "position": {
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                     "output_name": "output1"
                 }
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@@ -437,8 +340,8 @@
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             "position": {
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-                "top": 516.84375
+                "left": 1821.3783868183484,
+                "top": 482.19337215633186
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@@ -461,14 +364,14 @@
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@@ -482,7 +385,7 @@
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+                "left": 2001.9694561709443,
                 "top": 0
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@@ -513,162 +416,59 @@
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-            "label": "remove > + lowercase",
-            "name": "Text transformation",
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                 }
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-            "name": "Replace",
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+            "name": "Cut",
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-                    "type": "input"
+                    "name": "out_file1",
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-            "tool_version": "9.3+galaxy1",
+            "tool_id": "Cut1",
+            "tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.0.2",
             "type": "tool",
-            "uuid": "c37db543-a966-4ed2-88b9-87b317465144",
+            "uuid": "8cc3e58f-2940-454a-9cf6-b32c1ab19016",
             "when": null,
             "workflow_outputs": []
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+        "10": {
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             "errors": null,
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+            "id": 10,
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                     {
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-                        "output_name": "outfile"
+                        "id": 9,
+                        "output_name": "out_file1"
                     }
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@@ -682,13 +482,13 @@
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+                "left": 2538.6178936709443,
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@@ -706,18 +506,18 @@
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@@ -731,7 +531,7 @@
                 }
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+                "left": 2977.7819561709443,
                 "top": 798.078125
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@@ -759,6 +559,6 @@
     "tags": [
         "VGP_curated"
     ],
-    "uuid": "3f6673a2-caf4-4156-b5da-cc6bde2ddc8d",
-    "version": 8
+    "uuid": "aa4960d9-198d-4990-a393-a98efcd3070a",
+    "version": 3
 }
\ 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 ee2feefeb..f9eaf2e64 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
 
+## [0.3] 2024-08-26
+
+- Changed the regex to only change the sequences. The workflow is now more robust to different (non VGP) scaffold names and VGP names with prefixes. 
+- Reduce the number of steps in the workflow. 
+
 ## [0.2] 2024-08-15
 
 - Bug Fix: a missing regex caused the list of contaminants to empty out and the contaminants were not removed.