diff --git a/modules/nf-core/modkit/bedmethyltobigwig/environment.yml b/modules/nf-core/modkit/bedmethyltobigwig/environment.yml
index 074604f01e3a..f4a14f4abb43 100644
--- a/modules/nf-core/modkit/bedmethyltobigwig/environment.yml
+++ b/modules/nf-core/modkit/bedmethyltobigwig/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ont-modkit=0.5.0"
+  - "bioconda::ont-modkit=0.6.0"
diff --git a/modules/nf-core/modkit/bedmethyltobigwig/main.nf b/modules/nf-core/modkit/bedmethyltobigwig/main.nf
index d51fb94e8a0f..dd0737d7dc2f 100644
--- a/modules/nf-core/modkit/bedmethyltobigwig/main.nf
+++ b/modules/nf-core/modkit/bedmethyltobigwig/main.nf
@@ -4,8 +4,8 @@ process MODKIT_BEDMETHYLTOBIGWIG {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/30/30413db983a1908edc096dcd8a31e7c26363b2010c5293e6bf59c0cef5d4a88a/data':
-        'biocontainers/ont-modkit:0.5.0--hcdda2d0_1' }"
+        'https://depot.galaxyproject.org/singularity/ont-modkit:0.6.0--hcdda2d0_0':
+        'biocontainers/ont-modkit:0.6.0--hcdda2d0_0' }"
 
     input:
     tuple val(meta),  path(bedmethyl)
diff --git a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap
index 7fedc4e7d057..d3ebb75cfbcd 100644
--- a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap
+++ b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,4322e3ce001be128a402386e9215e578"
+                    "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b"
                 ],
                 "bw": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,4322e3ce001be128a402386e9215e578"
+                    "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-08-28T08:39:57.052601865"
+        "timestamp": "2025-12-11T09:38:52.912687858"
     },
     "homo sapiens - bedmethyl, fai, list": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,4322e3ce001be128a402386e9215e578"
+                    "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b"
                 ],
                 "bw": [
                     [
@@ -55,15 +55,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,4322e3ce001be128a402386e9215e578"
+                    "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-08-28T08:39:35.618444189"
+        "timestamp": "2025-12-11T09:38:35.894897541"
     },
     "homo sapiens - bedmethyl, fai, string": {
         "content": [
@@ -77,7 +77,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,4322e3ce001be128a402386e9215e578"
+                    "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b"
                 ],
                 "bw": [
                     [
@@ -88,14 +88,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,4322e3ce001be128a402386e9215e578"
+                    "versions.yml:md5,c8f7017057430cb3694736c606c8eb6b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-08-28T08:39:46.624865666"
+        "timestamp": "2025-12-11T09:38:44.647742811"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/modkit/callmods/environment.yml b/modules/nf-core/modkit/callmods/environment.yml
index 74d7fb53a557..07f12cf97a7b 100644
--- a/modules/nf-core/modkit/callmods/environment.yml
+++ b/modules/nf-core/modkit/callmods/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::ont-modkit=0.5.0
+  - bioconda::ont-modkit=0.6.0
diff --git a/modules/nf-core/modkit/callmods/main.nf b/modules/nf-core/modkit/callmods/main.nf
index d9b5d7727a44..b0b1bea15ee6 100644
--- a/modules/nf-core/modkit/callmods/main.nf
+++ b/modules/nf-core/modkit/callmods/main.nf
@@ -4,8 +4,8 @@ process MODKIT_CALLMODS {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://depot.galaxyproject.org/singularity/ont-modkit:0.5.0--hcdda2d0_2'
-        : 'biocontainers/ont-modkit:0.5.0--hcdda2d0_2'}"
+        ? 'https://depot.galaxyproject.org/singularity/ont-modkit:0.6.0--hcdda2d0_0'
+        : 'biocontainers/ont-modkit:0.6.0--hcdda2d0_0'}"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/modkit/callmods/tests/main.nf.test.snap b/modules/nf-core/modkit/callmods/tests/main.nf.test.snap
index 834706a5c162..18251a71992e 100644
--- a/modules/nf-core/modkit/callmods/tests/main.nf.test.snap
+++ b/modules/nf-core/modkit/callmods/tests/main.nf.test.snap
@@ -35,7 +35,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,03e4a3c3498e53548d4fd0deb17a425f"
+                    "versions.yml:md5,90d284c04e15a618a6b9f893a889630a"
                 ],
                 "bam": [
                     [
@@ -54,19 +54,19 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,03e4a3c3498e53548d4fd0deb17a425f"
+                    "versions.yml:md5,90d284c04e15a618a6b9f893a889630a"
                 ]
             },
             {
                 "MODKIT_CALLMODS": {
-                    "modkit": "0.5.0"
+                    "modkit": "0.6.0"
                 }
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-10-13T16:38:07.173458603"
+        "timestamp": "2025-12-10T15:07:44.990852881"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/modkit/repair/environment.yml b/modules/nf-core/modkit/repair/environment.yml
index 074604f01e3a..f4a14f4abb43 100644
--- a/modules/nf-core/modkit/repair/environment.yml
+++ b/modules/nf-core/modkit/repair/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ont-modkit=0.5.0"
+  - "bioconda::ont-modkit=0.6.0"
diff --git a/modules/nf-core/modkit/repair/main.nf b/modules/nf-core/modkit/repair/main.nf
index 8f39f075900b..0a1ecc75109f 100644
--- a/modules/nf-core/modkit/repair/main.nf
+++ b/modules/nf-core/modkit/repair/main.nf
@@ -4,8 +4,8 @@ process MODKIT_REPAIR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ont-modkit:0.5.0--hcdda2d0_1':
-        'biocontainers/ont-modkit:0.5.0--hcdda2d0_1' }"
+        'https://depot.galaxyproject.org/singularity/ont-modkit:0.6.0--hcdda2d0_0':
+        'biocontainers/ont-modkit:0.6.0--hcdda2d0_0' }"
 
     input:
     tuple val(meta), path(before_trim), path(after_trim)
diff --git a/modules/nf-core/modkit/repair/meta.yml b/modules/nf-core/modkit/repair/meta.yml
index e76d2b8c2dde..5a88737fb1d9 100644
--- a/modules/nf-core/modkit/repair/meta.yml
+++ b/modules/nf-core/modkit/repair/meta.yml
@@ -1,7 +1,6 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "modkit_repair"
-description: Modkit is a bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data. The command `modkit reapir` is used for repairing the MM/ML tags on trimmed or hard-clipped ONT reads.
-
+description: Repair the MM/ML tags on trimmed or hard-clipped ONT reads using untrimmed ONT reads.
 keywords:
   - methylation
   - ont
diff --git a/modules/nf-core/modkit/repair/tests/main.nf.test.snap b/modules/nf-core/modkit/repair/tests/main.nf.test.snap
index 72907800060d..bb455c1bc5b3 100644
--- a/modules/nf-core/modkit/repair/tests/main.nf.test.snap
+++ b/modules/nf-core/modkit/repair/tests/main.nf.test.snap
@@ -35,7 +35,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,3afdad70e5d4dcc2515104fe24fb32b2"
+                    "versions.yml:md5,5eac7da8523b0c92aeffd6da42bf161a"
                 ],
                 "bam": [
                     [
@@ -54,19 +54,19 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3afdad70e5d4dcc2515104fe24fb32b2"
+                    "versions.yml:md5,5eac7da8523b0c92aeffd6da42bf161a"
                 ]
             },
             {
                 "MODKIT_REPAIR": {
-                    "modkit": "0.5.0"
+                    "modkit": "0.6.0"
                 }
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-09-26T14:41:41.621896549"
+        "timestamp": "2025-12-10T15:10:54.452622058"
     }
 }
\ No newline at end of file