diff --git a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md
index cb5a34c219..3da2f9d0e6 100644
--- a/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md
+++ b/workflows/genome-assembly/bacterial-genome-assembly/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Changelog
 
+## [2.1] - 2026-04-15
+
+### Manual update
+
+* Add CONVERTER_gz_to_uncompressed tool box because some fastq.gz files cause errors, uncompressing them resolves the issue
+
 ## [2.0.1] - 2025-12-01
 
 ### Automatic update
diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
index 71ce05c1ae..db2041f8f1 100644
--- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
+++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly.ga
@@ -55,13 +55,13 @@
             "outputs": [],
             "position": {
                 "left": 0,
-                "top": 0
+                "top": 70.89967996986218
             },
             "tool_id": null,
             "tool_state": "{\"optional\": false, \"format\": [\"fastq\", \"fastq.gz\", \"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}",
             "tool_version": null,
             "type": "data_input",
-            "uuid": "40f70938-12cb-4908-875a-28085631e951",
+            "uuid": "ef11c18d-87d0-4676-a4a2-8ce0be6f097a",
             "when": null,
             "workflow_outputs": []
         },
@@ -82,31 +82,125 @@
             "outputs": [],
             "position": {
                 "left": 1.5420743426057233,
-                "top": 152.99910549496644
+                "top": 223.89878546482862
             },
             "tool_id": null,
             "tool_state": "{\"optional\": false, \"format\": [\"fastq\", \"fastq.gz\", \"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}",
             "tool_version": null,
             "type": "data_input",
-            "uuid": "9542727a-8573-40b8-ad09-d0eb45231e3d",
+            "uuid": "64671947-d1a9-4858-84bc-81d29d626b62",
             "when": null,
             "workflow_outputs": []
         },
         "2": {
-            "annotation": "genome assembly with shovill tool",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2",
+            "annotation": "Uncompress to avoid shovill error",
+            "content_id": "CONVERTER_gz_to_uncompressed",
             "errors": null,
             "id": 2,
             "input_connections": {
-                "library|R1": {
+                "input1": {
                     "id": 0,
                     "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": "Uncompress fastq file forward",
+            "name": "Convert compressed file to uncompressed.",
+            "outputs": [
+                {
+                    "name": "output1",
+                    "type": "auto"
+                }
+            ],
+            "position": {
+                "left": 289.15442190904133,
+                "top": 0
+            },
+            "post_job_actions": {
+                "ChangeDatatypeActionoutput1": {
+                    "action_arguments": {
+                        "newtype": "fastq"
+                    },
+                    "action_type": "ChangeDatatypeAction",
+                    "output_name": "output1"
                 },
-                "library|R2": {
+                "HideDatasetActionoutput1": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "output1"
+                }
+            },
+            "tool_id": "CONVERTER_gz_to_uncompressed",
+            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_uuid": null,
+            "tool_version": "1.0.0",
+            "type": "tool",
+            "uuid": "2e3ca490-0b27-49b6-825f-b47df15123d4",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "3": {
+            "annotation": "Uncompress to avoid shovill error",
+            "content_id": "CONVERTER_gz_to_uncompressed",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "input1": {
                     "id": 1,
                     "output_name": "output"
                 }
             },
+            "inputs": [],
+            "label": "Uncompress fastq file reverse",
+            "name": "Convert compressed file to uncompressed.",
+            "outputs": [
+                {
+                    "name": "output1",
+                    "type": "auto"
+                }
+            ],
+            "position": {
+                "left": 284.5308378684377,
+                "top": 223.19489236504248
+            },
+            "post_job_actions": {
+                "ChangeDatatypeActionoutput1": {
+                    "action_arguments": {
+                        "newtype": "fastq"
+                    },
+                    "action_type": "ChangeDatatypeAction",
+                    "output_name": "output1"
+                },
+                "HideDatasetActionoutput1": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "output1"
+                }
+            },
+            "tool_id": "CONVERTER_gz_to_uncompressed",
+            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_uuid": null,
+            "tool_version": "1.0.0",
+            "type": "tool",
+            "uuid": "0cb2e893-d780-4fa4-8572-5465c1631d85",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "4": {
+            "annotation": "genome assembly with shovill tool",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2",
+            "errors": null,
+            "id": 4,
+            "input_connections": {
+                "library|R1": {
+                    "id": 2,
+                    "output_name": "output1"
+                },
+                "library|R2": {
+                    "id": 3,
+                    "output_name": "output1"
+                }
+            },
             "inputs": [
                 {
                     "description": "runtime parameter for tool Shovill",
@@ -138,8 +232,8 @@
                 }
             ],
             "position": {
-                "left": 308.4719663659007,
-                "top": 104.1423404663812
+                "left": 558.7716084796539,
+                "top": 126.51841492906757
             },
             "post_job_actions": {
                 "ChangeDatatypeActionbamfiles": {
@@ -216,39 +310,39 @@
             "tool_state": "{\"adv\": {\"namefmt\": \"contig%05d\", \"depth\": \"100\", \"gsize\": \"\", \"kmers\": \"\", \"opts\": \"\", \"keep_files\": {\"nocorr\": \"yes_correction\", \"__current_case__\": 1, \"keepfiles\": true}, \"minlen\": \"0\", \"mincov\": \"2\"}, \"assembler\": \"spades\", \"library\": {\"lib_type\": \"paired\", \"__current_case__\": 0, \"R1\": {\"__class__\": \"ConnectedValue\"}, \"R2\": {\"__class__\": \"ConnectedValue\"}}, \"log\": true, \"trim\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "1.1.0+galaxy2",
             "type": "tool",
-            "uuid": "e7b73002-c415-445b-9e00-51f45caefe88",
+            "uuid": "c2e0573d-b168-48d4-b156-e4d54678e65b",
             "when": null,
             "workflow_outputs": [
                 {
                     "label": "shovill_alignment_bam",
                     "output_name": "bamfiles",
-                    "uuid": "4d3aa9b6-a537-4897-b694-5b5095316a72"
+                    "uuid": "66ae211c-f0dd-4d7d-b1b3-040811348905"
                 },
                 {
                     "label": "shovill_contigs_graph",
                     "output_name": "contigs_graph",
-                    "uuid": "412b46ef-12e7-4597-8917-a6b327749f58"
-                },
-                {
-                    "label": "shovill_logfile",
-                    "output_name": "shovill_std_log",
-                    "uuid": "0013a7ae-d67d-4223-893f-9ef43182908d"
+                    "uuid": "ad37b271-dfeb-4ec8-b26f-a8123230de61"
                 },
                 {
                     "label": "shovill_contigs_fasta",
                     "output_name": "contigs",
-                    "uuid": "817d1c97-960d-4d00-bc92-4692300dd4df"
+                    "uuid": "27984b4f-1fe8-49e8-94b4-c62b9d51276b"
+                },
+                {
+                    "label": "shovill_logfile",
+                    "output_name": "shovill_std_log",
+                    "uuid": "67fe0656-6390-4003-8a6c-0dfc01c02c15"
                 }
             ]
         },
-        "3": {
+        "5": {
             "annotation": "bandage_contig_graph_stats",
             "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2",
             "errors": null,
-            "id": 3,
+            "id": 5,
             "input_connections": {
                 "input_file": {
-                    "id": 2,
+                    "id": 4,
                     "output_name": "contigs_graph"
                 }
             },
@@ -263,7 +357,7 @@
             ],
             "position": {
                 "left": 877.6030241930225,
-                "top": 295.54813439028237
+                "top": 366.44781436014455
             },
             "post_job_actions": {
                 "RenameDatasetActionoutfile": {
@@ -291,24 +385,24 @@
             "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"tsv\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2022.09+galaxy2",
             "type": "tool",
-            "uuid": "9a92c323-4df3-4cb7-8ca6-abdf73de0ff3",
+            "uuid": "d7a795a3-165d-4c5b-a275-75d15d6df7e7",
             "when": null,
             "workflow_outputs": [
                 {
                     "label": "bandage_contig_graph_stats",
                     "output_name": "outfile",
-                    "uuid": "db1a4fc2-5394-421c-a1a8-2907bec1c157"
+                    "uuid": "cd62c87f-7dcd-4db5-a0a4-b592801640db"
                 }
             ]
         },
-        "4": {
+        "6": {
             "annotation": "bandage_contig_graph_plot",
             "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
             "errors": null,
-            "id": 4,
+            "id": 6,
             "input_connections": {
                 "input_file": {
-                    "id": 2,
+                    "id": 4,
                     "output_name": "contigs_graph"
                 }
             },
@@ -323,7 +417,7 @@
             ],
             "position": {
                 "left": 890.2572810380926,
-                "top": 507.17892819971473
+                "top": 578.0786081695769
             },
             "post_job_actions": {
                 "RenameDatasetActionoutfile": {
@@ -351,24 +445,24 @@
             "tool_state": "{\"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": false, \"names\": false, \"nodewidth\": null, \"output_format\": \"svg\", \"width\": \"1000\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "2022.09+galaxy4",
             "type": "tool",
-            "uuid": "4482449a-7009-475d-9095-5d08fd465fed",
+            "uuid": "a73dc0bf-77af-48bb-a8a2-31da9ddd8633",
             "when": null,
             "workflow_outputs": [
                 {
                     "label": "bandage_contig_graph_plot",
                     "output_name": "outfile",
-                    "uuid": "883cb5ea-7305-4ce7-bf5d-702bbaa23037"
+                    "uuid": "bae1f176-05ad-41ca-871e-1ea243d041cf"
                 }
             ]
         },
-        "5": {
+        "7": {
             "annotation": "ToolDistillator extracts results from tools and creates a JSON file for each tool",
             "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0",
             "errors": null,
-            "id": 5,
+            "id": 7,
             "input_connections": {
                 "tool_section|tools_0|select_tool|input": {
-                    "id": 2,
+                    "id": 4,
                     "output_name": "contigs"
                 }
             },
@@ -383,7 +477,7 @@
             ],
             "position": {
                 "left": 1116.121721297883,
-                "top": 61.60416487623325
+                "top": 132.50384484609543
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput_json": {
@@ -411,33 +505,28 @@
             "tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"shovill\", \"__current_case__\": 36, \"input\": {\"__class__\": \"RuntimeValue\"}, \"contig_graph_path\": {\"__class__\": \"RuntimeValue\"}, \"bam_file_path\": {\"__class__\": \"RuntimeValue\"}, \"origin\": {\"origin\": \"false\", \"__current_case__\": 1}, \"reference_database_version\": null}}]}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
             "tool_version": "1.0.4+galaxy0",
             "type": "tool",
-            "uuid": "12e27969-f4a9-47c8-a561-d7145ac83a0a",
+            "uuid": "ade26a98-9ba1-44b2-ab50-83d6c4815224",
             "when": null,
             "workflow_outputs": [
                 {
                     "label": "tooldistillator_results_assembly",
                     "output_name": "output_json",
-                    "uuid": "a5890d50-4eb8-4941-8af7-8c2eb91e4cb6"
+                    "uuid": "e1e8324d-11a4-4552-a849-1610555c9f5b"
                 }
             ]
         },
-        "6": {
+        "8": {
             "annotation": "ToolDistillator summarize groups all JSON file into a unique JSON file",
             "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0",
             "errors": null,
-            "id": 6,
+            "id": 8,
             "input_connections": {
                 "summarize_data": {
-                    "id": 5,
+                    "id": 7,
                     "output_name": "output_json"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool ToolDistillator Summarize",
-                    "name": "summarize_data"
-                }
-            ],
+            "inputs": [],
             "label": "ToolDistillator summarize",
             "name": "ToolDistillator Summarize",
             "outputs": [
@@ -448,7 +537,7 @@
             ],
             "position": {
                 "left": 1355.983929150398,
-                "top": 346.47653923847076
+                "top": 417.37621920833294
             },
             "post_job_actions": {
                 "RenameDatasetActionsummary_json": {
@@ -476,13 +565,13 @@
             "tool_state": "{\"summarize_data\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
             "tool_version": "1.0.4+galaxy0",
             "type": "tool",
-            "uuid": "e12a9c8d-3bf6-4f7e-8007-ba25d5722ce2",
+            "uuid": "3eb18b72-fb31-4d56-98ad-8f27180d7c58",
             "when": null,
             "workflow_outputs": [
                 {
                     "label": "tooldistillator_summarize_assembly",
                     "output_name": "summary_json",
-                    "uuid": "ca314221-a603-4908-aa12-fbd6882a1586"
+                    "uuid": "a77f8316-d3b3-49ed-b0ad-103dcb216f5d"
                 }
             ]
         }
@@ -496,7 +585,7 @@
         "quality",
         "ABRomics"
     ],
-    "uuid": "14fc2baa-a9fb-4e90-a8ec-f542faf1d8c2",
+    "uuid": "d7aafe74-9984-4828-a2da-101c72ffe2b6",
     "version": 1,
-    "release": "2.0.1"
+    "release": "2.1"
 }
\ No newline at end of file