diff --git a/modules/nf-core/ampcombi2/cluster/environment.yml b/modules/nf-core/ampcombi2/cluster/environment.yml
index 420c955bfd2..f9c25b04a1d 100644
--- a/modules/nf-core/ampcombi2/cluster/environment.yml
+++ b/modules/nf-core/ampcombi2/cluster/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ampcombi=0.2.2"
+  - "bioconda::ampcombi=2.0.1"
diff --git a/modules/nf-core/ampcombi2/cluster/main.nf b/modules/nf-core/ampcombi2/cluster/main.nf
index 90495dba4b6..98a19a966c7 100644
--- a/modules/nf-core/ampcombi2/cluster/main.nf
+++ b/modules/nf-core/ampcombi2/cluster/main.nf
@@ -4,8 +4,8 @@ process AMPCOMBI2_CLUSTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ampcombi:0.2.2--pyhdfd78af_0':
-        'biocontainers/ampcombi:0.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
+        'biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"
 
     input:
     path(summary_file)
diff --git a/modules/nf-core/ampcombi2/cluster/tests/main.nf.test.snap b/modules/nf-core/ampcombi2/cluster/tests/main.nf.test.snap
index f4123c76322..fd79a83b92a 100644
--- a/modules/nf-core/ampcombi2/cluster/tests/main.nf.test.snap
+++ b/modules/nf-core/ampcombi2/cluster/tests/main.nf.test.snap
@@ -4,14 +4,14 @@
             true,
             true,
             [
-                "versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
+                "versions.yml:md5,b629089d44775078dce5e664a455422b"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-24T12:11:40.928513749"
+        "timestamp": "2024-12-03T07:57:01.869983435"
     },
     "ampcombi2_cluster - metagenome - stub": {
         "content": [
@@ -26,7 +26,7 @@
                     "Ampcombi_cluster.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "3": [
-                    "versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
+                    "versions.yml:md5,b629089d44775078dce5e664a455422b"
                 ],
                 "cluster_tsv": [
                     "Ampcombi_summary_cluster.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -38,14 +38,14 @@
                     "Ampcombi_summary_cluster_representative_seq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "versions": [
-                    "versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
+                    "versions.yml:md5,b629089d44775078dce5e664a455422b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-24T12:12:08.780718892"
+        "timestamp": "2024-12-03T07:57:23.939137628"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/ampcombi2/complete/environment.yml b/modules/nf-core/ampcombi2/complete/environment.yml
index 420c955bfd2..f9c25b04a1d 100644
--- a/modules/nf-core/ampcombi2/complete/environment.yml
+++ b/modules/nf-core/ampcombi2/complete/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ampcombi=0.2.2"
+  - "bioconda::ampcombi=2.0.1"
diff --git a/modules/nf-core/ampcombi2/complete/main.nf b/modules/nf-core/ampcombi2/complete/main.nf
index 0e4d5d53738..98f62347ba2 100644
--- a/modules/nf-core/ampcombi2/complete/main.nf
+++ b/modules/nf-core/ampcombi2/complete/main.nf
@@ -4,8 +4,8 @@ process AMPCOMBI2_COMPLETE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ampcombi:0.2.2--pyhdfd78af_0':
-        'biocontainers/ampcombi:0.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
+        'biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"
 
     input:
     path(summaries)
diff --git a/modules/nf-core/ampcombi2/complete/tests/main.nf.test.snap b/modules/nf-core/ampcombi2/complete/tests/main.nf.test.snap
index cd8fa18f919..87435e5b931 100644
--- a/modules/nf-core/ampcombi2/complete/tests/main.nf.test.snap
+++ b/modules/nf-core/ampcombi2/complete/tests/main.nf.test.snap
@@ -6,39 +6,39 @@
                     "Ampcombi_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "1": [
-                    
+
                 ],
                 "2": [
-                    "versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
+                    "versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
                 ],
                 "log": [
-                    
+
                 ],
                 "tsv": [
                     "Ampcombi_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "versions": [
-                    "versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
+                    "versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-29T11:55:16.030399422"
+        "timestamp": "2024-12-03T07:57:53.385349848"
     },
     "ampcombi2_complete - contigs": {
         "content": [
             true,
             [
-                "versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
+                "versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-29T11:54:54.334224301"
+        "timestamp": "2024-12-03T07:57:40.263912946"
     }
-}
\ No newline at end of file
+}