diff --git a/modules/nf-core/seqkit/concat/environment.yml b/modules/nf-core/seqkit/concat/environment.yml
index 4f8058a9a57..160a67c08e8 100644
--- a/modules/nf-core/seqkit/concat/environment.yml
+++ b/modules/nf-core/seqkit/concat/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::seqkit=2.8.1"
+  - "bioconda::seqkit=2.9.0"
diff --git a/modules/nf-core/seqkit/concat/main.nf b/modules/nf-core/seqkit/concat/main.nf
index bb9eec1e390..d10d9780fb7 100644
--- a/modules/nf-core/seqkit/concat/main.nf
+++ b/modules/nf-core/seqkit/concat/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_CONCAT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(input, stageAs: 'in/*')
diff --git a/modules/nf-core/seqkit/concat/tests/main.nf.test.snap b/modules/nf-core/seqkit/concat/tests/main.nf.test.snap
index 1010d6988b6..5f85418c6d8 100644
--- a/modules/nf-core/seqkit/concat/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/concat/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "sarscov2 and human primers - fasta": {
         "content": [
             [
-                "versions.yml:md5,32d898698c9224f989b9527fe0b948d4"
+                "versions.yml:md5,13b312c8ca94f9c6460ffc759a5c79c9"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:33:12.38186745"
+        "timestamp": "2025-01-15T15:06:45.246143"
     },
     "sarscov2 and human primers - fasta - stub": {
         "content": [
@@ -23,7 +23,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,32d898698c9224f989b9527fe0b948d4"
+                    "versions.yml:md5,13b312c8ca94f9c6460ffc759a5c79c9"
                 ],
                 "fastx": [
                     [
@@ -34,14 +34,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,32d898698c9224f989b9527fe0b948d4"
+                    "versions.yml:md5,13b312c8ca94f9c6460ffc759a5c79c9"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:33:22.533226274"
+        "timestamp": "2025-01-15T15:06:49.428563"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/fq2fa/environment.yml b/modules/nf-core/seqkit/fq2fa/environment.yml
index 41f3e7de43d..1f93892f485 100644
--- a/modules/nf-core/seqkit/fq2fa/environment.yml
+++ b/modules/nf-core/seqkit/fq2fa/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/fq2fa/main.nf b/modules/nf-core/seqkit/fq2fa/main.nf
index 77462ad0c5a..1707dbc5fe9 100644
--- a/modules/nf-core/seqkit/fq2fa/main.nf
+++ b/modules/nf-core/seqkit/fq2fa/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_FQ2FA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0' :
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' :
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastq)
diff --git a/modules/nf-core/seqkit/fq2fa/tests/main.nf.test.snap b/modules/nf-core/seqkit/fq2fa/tests/main.nf.test.snap
index b10ff751508..4d39a7e9e37 100644
--- a/modules/nf-core/seqkit/fq2fa/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/fq2fa/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,70efc6839fd6443ee9116c082a730f72"
+                    "versions.yml:md5,9799aeba106e1fd61b65fd876eabd863"
                 ],
                 "fasta": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,70efc6839fd6443ee9116c082a730f72"
+                    "versions.yml:md5,9799aeba106e1fd61b65fd876eabd863"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-13T08:56:21.234724552"
+        "timestamp": "2025-01-15T15:07:44.366504"
     },
     "sarscov2 - bam": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,70efc6839fd6443ee9116c082a730f72"
+                    "versions.yml:md5,9799aeba106e1fd61b65fd876eabd863"
                 ],
                 "fasta": [
                     [
@@ -59,14 +59,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,70efc6839fd6443ee9116c082a730f72"
+                    "versions.yml:md5,9799aeba106e1fd61b65fd876eabd863"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-13T08:55:54.648865102"
+        "timestamp": "2025-01-15T15:07:40.187352"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/grep/environment.yml b/modules/nf-core/seqkit/grep/environment.yml
index 41f3e7de43d..1f93892f485 100644
--- a/modules/nf-core/seqkit/grep/environment.yml
+++ b/modules/nf-core/seqkit/grep/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/grep/main.nf b/modules/nf-core/seqkit/grep/main.nf
index ce6dc2422c1..9dc2a8926a8 100644
--- a/modules/nf-core/seqkit/grep/main.nf
+++ b/modules/nf-core/seqkit/grep/main.nf
@@ -5,8 +5,8 @@ process SEQKIT_GREP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(sequence)
diff --git a/modules/nf-core/seqkit/grep/tests/main.nf.test.snap b/modules/nf-core/seqkit/grep/tests/main.nf.test.snap
index 2ab6f4b84e7..26a1abf7c3e 100644
--- a/modules/nf-core/seqkit/grep/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/grep/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ],
                 "filter": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:33:47.542049206"
+        "timestamp": "2025-01-15T15:08:46.340613"
     },
     "with_pattern": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ],
                 "filter": [
                     [
@@ -59,15 +59,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:38:28.77443193"
+        "timestamp": "2025-01-15T15:08:55.077598"
     },
     "with_file - stub": {
         "content": [
@@ -82,7 +82,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ],
                 "filter": [
                     [
@@ -94,14 +94,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:34:12.85678016"
+        "timestamp": "2025-01-15T15:09:03.009991"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/pair/environment.yml b/modules/nf-core/seqkit/pair/environment.yml
index 41f3e7de43d..1f93892f485 100644
--- a/modules/nf-core/seqkit/pair/environment.yml
+++ b/modules/nf-core/seqkit/pair/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/pair/main.nf b/modules/nf-core/seqkit/pair/main.nf
index df0b3a5d031..258a62fde51 100644
--- a/modules/nf-core/seqkit/pair/main.nf
+++ b/modules/nf-core/seqkit/pair/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_PAIR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/seqkit/pair/tests/main.nf.test.snap b/modules/nf-core/seqkit/pair/tests/main.nf.test.snap
index c25d745fe4c..c301b744f75 100644
--- a/modules/nf-core/seqkit/pair/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/pair/tests/main.nf.test.snap
@@ -18,7 +18,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,77fbea93a3c50ec0f6da886d9849622e"
+                    "versions.yml:md5,8281825c657e9ddabacfeb0d1c07f11e"
                 ],
                 "reads": [
                     [
@@ -36,15 +36,15 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,77fbea93a3c50ec0f6da886d9849622e"
+                    "versions.yml:md5,8281825c657e9ddabacfeb0d1c07f11e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:11:09.767703292"
+        "timestamp": "2025-01-15T15:09:51.247775"
     },
     "sarscov2 - bam": {
         "content": [
@@ -65,7 +65,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,77fbea93a3c50ec0f6da886d9849622e"
+                    "versions.yml:md5,8281825c657e9ddabacfeb0d1c07f11e"
                 ],
                 "reads": [
                     [
@@ -83,14 +83,14 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,77fbea93a3c50ec0f6da886d9849622e"
+                    "versions.yml:md5,8281825c657e9ddabacfeb0d1c07f11e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-07T15:54:57.649454879"
+        "timestamp": "2025-01-15T15:09:46.914754"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/replace/environment.yml b/modules/nf-core/seqkit/replace/environment.yml
index 41f3e7de43d..1f93892f485 100644
--- a/modules/nf-core/seqkit/replace/environment.yml
+++ b/modules/nf-core/seqkit/replace/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf
index 70811c8bbd7..2da15bc02ae 100644
--- a/modules/nf-core/seqkit/replace/main.nf
+++ b/modules/nf-core/seqkit/replace/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_REPLACE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastx)
diff --git a/modules/nf-core/seqkit/replace/tests/main.nf.test.snap b/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
index 24e1887f86e..83625875b58 100644
--- a/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d0b955de076997af3989d2ce5b5417b6"
+                    "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
                 ],
                 "fastx": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d0b955de076997af3989d2ce5b5417b6"
+                    "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T11:10:12.100214525"
+        "timestamp": "2025-01-15T15:10:45.336609"
     },
     "sarscov2 - fasta - replace": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d0b955de076997af3989d2ce5b5417b6"
+                    "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
                 ],
                 "fastx": [
                     [
@@ -55,15 +55,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d0b955de076997af3989d2ce5b5417b6"
+                    "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-07T16:23:57.895160549"
+        "timestamp": "2025-01-15T15:10:36.722731"
     },
     "sarscov2 - fasta - uncomp": {
         "content": [
@@ -77,7 +77,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d0b955de076997af3989d2ce5b5417b6"
+                    "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
                 ],
                 "fastx": [
                     [
@@ -88,14 +88,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d0b955de076997af3989d2ce5b5417b6"
+                    "versions.yml:md5,edcad74f001a6cf3a54d2a99bd532b50"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-07T16:24:09.142463316"
+        "timestamp": "2025-01-15T15:10:41.090521"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/rmdup/environment.yml b/modules/nf-core/seqkit/rmdup/environment.yml
index 4f8058a9a57..160a67c08e8 100644
--- a/modules/nf-core/seqkit/rmdup/environment.yml
+++ b/modules/nf-core/seqkit/rmdup/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::seqkit=2.8.1"
+  - "bioconda::seqkit=2.9.0"
diff --git a/modules/nf-core/seqkit/rmdup/main.nf b/modules/nf-core/seqkit/rmdup/main.nf
index 410bb8366b1..f943a76fee2 100644
--- a/modules/nf-core/seqkit/rmdup/main.nf
+++ b/modules/nf-core/seqkit/rmdup/main.nf
@@ -5,8 +5,8 @@ process SEQKIT_RMDUP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastx)
diff --git a/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap b/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap
index 68c415cd9ce..4b2858daa1e 100644
--- a/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/rmdup/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,d2b8da3c114c2bd1c6606030df55b6aa"
+                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
                 ],
                 "fastx": [
                     [
@@ -38,15 +38,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2b8da3c114c2bd1c6606030df55b6aa"
+                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-27T19:40:01.6034"
+        "timestamp": "2025-01-15T15:12:04.249165"
     },
     "sarscov2-test_1_fastq_gz": {
         "content": [
@@ -68,7 +68,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,d2b8da3c114c2bd1c6606030df55b6aa"
+                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
                 ],
                 "fastx": [
                     [
@@ -87,15 +87,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2b8da3c114c2bd1c6606030df55b6aa"
+                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-27T19:37:48.551195"
+        "timestamp": "2025-01-15T15:11:57.07272"
     },
     "sarscov2-genome_fasta": {
         "content": [
@@ -117,7 +117,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,d2b8da3c114c2bd1c6606030df55b6aa"
+                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
                 ],
                 "fastx": [
                     [
@@ -136,17 +136,17 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2b8da3c114c2bd1c6606030df55b6aa"
+                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-27T19:37:38.821528"
+        "timestamp": "2025-01-15T15:11:44.13147"
     },
-    "sarscov2-genome_fasta_gz": {
+    "repeated-fasta": {
         "content": [
             {
                 "0": [
@@ -154,7 +154,7 @@
                         {
                             "id": "test"
                         },
-                        "test.fasta.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
+                        "test.fasta:md5,7510a742291241e7d7556bf720caf65c"
                     ]
                 ],
                 "1": [
@@ -162,18 +162,18 @@
                         {
                             "id": "test"
                         },
-                        "test.log:md5,a41135cfe024baaf42f135583fe73f0d"
+                        "test.log:md5,314c0aaef0f832a217a3f6ce3f8bc117"
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,d2b8da3c114c2bd1c6606030df55b6aa"
+                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
                 ],
                 "fastx": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.fasta.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
+                        "test.fasta:md5,7510a742291241e7d7556bf720caf65c"
                     ]
                 ],
                 "log": [
@@ -181,21 +181,21 @@
                         {
                             "id": "test"
                         },
-                        "test.log:md5,a41135cfe024baaf42f135583fe73f0d"
+                        "test.log:md5,314c0aaef0f832a217a3f6ce3f8bc117"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2b8da3c114c2bd1c6606030df55b6aa"
+                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-27T19:37:43.723054"
+        "timestamp": "2025-01-15T15:11:48.203975"
     },
-    "repeated-fasta": {
+    "sarscov2-genome_fasta_gz": {
         "content": [
             {
                 "0": [
@@ -203,7 +203,7 @@
                         {
                             "id": "test"
                         },
-                        "test.fasta:md5,7510a742291241e7d7556bf720caf65c"
+                        "test.fasta.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
                     ]
                 ],
                 "1": [
@@ -211,18 +211,18 @@
                         {
                             "id": "test"
                         },
-                        "test.log:md5,314c0aaef0f832a217a3f6ce3f8bc117"
+                        "test.log:md5,a41135cfe024baaf42f135583fe73f0d"
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,d2b8da3c114c2bd1c6606030df55b6aa"
+                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
                 ],
                 "fastx": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.fasta:md5,7510a742291241e7d7556bf720caf65c"
+                        "test.fasta.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
                     ]
                 ],
                 "log": [
@@ -230,18 +230,18 @@
                         {
                             "id": "test"
                         },
-                        "test.log:md5,314c0aaef0f832a217a3f6ce3f8bc117"
+                        "test.log:md5,a41135cfe024baaf42f135583fe73f0d"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d2b8da3c114c2bd1c6606030df55b6aa"
+                    "versions.yml:md5,9855ca606b68cb8c32718a1249488688"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-27T19:52:34.545807"
+        "timestamp": "2025-01-15T15:11:52.657459"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/seq/environment.yml b/modules/nf-core/seqkit/seq/environment.yml
index 4f8058a9a57..160a67c08e8 100644
--- a/modules/nf-core/seqkit/seq/environment.yml
+++ b/modules/nf-core/seqkit/seq/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::seqkit=2.8.1"
+  - "bioconda::seqkit=2.9.0"
diff --git a/modules/nf-core/seqkit/seq/main.nf b/modules/nf-core/seqkit/seq/main.nf
index d7d38fc882c..9d76da213c0 100644
--- a/modules/nf-core/seqkit/seq/main.nf
+++ b/modules/nf-core/seqkit/seq/main.nf
@@ -5,8 +5,8 @@ process SEQKIT_SEQ {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastx)
diff --git a/modules/nf-core/seqkit/seq/tests/main.nf.test.snap b/modules/nf-core/seqkit/seq/tests/main.nf.test.snap
index e6910966322..68171935f33 100644
--- a/modules/nf-core/seqkit/seq/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/seq/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,34894c4efa5e10a923e78975a3d260dd"
+                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
                 ],
                 "fastx": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,34894c4efa5e10a923e78975a3d260dd"
+                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:52:18.220051903"
+        "timestamp": "2025-01-15T15:13:34.513457"
     },
     "sarscov2-test_1_fastq_gz": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,34894c4efa5e10a923e78975a3d260dd"
+                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
                 ],
                 "fastx": [
                     [
@@ -55,15 +55,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,34894c4efa5e10a923e78975a3d260dd"
+                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:51:55.607826581"
+        "timestamp": "2025-01-15T15:13:27.316329"
     },
     "sarscov2-genome_fasta": {
         "content": [
@@ -77,7 +77,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,34894c4efa5e10a923e78975a3d260dd"
+                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
                 ],
                 "fastx": [
                     [
@@ -88,15 +88,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,34894c4efa5e10a923e78975a3d260dd"
+                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:51:27.717072933"
+        "timestamp": "2025-01-15T15:13:18.463038"
     },
     "sarscov2-genome_fasta_gz": {
         "content": [
@@ -110,7 +110,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,34894c4efa5e10a923e78975a3d260dd"
+                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
                 ],
                 "fastx": [
                     [
@@ -121,14 +121,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,34894c4efa5e10a923e78975a3d260dd"
+                    "versions.yml:md5,eeb475e557ef671d4b58e11f82d2448e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:51:37.917560104"
+        "timestamp": "2025-01-15T15:13:22.960973"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/sliding/environment.yml b/modules/nf-core/seqkit/sliding/environment.yml
index 41f3e7de43d..1f93892f485 100644
--- a/modules/nf-core/seqkit/sliding/environment.yml
+++ b/modules/nf-core/seqkit/sliding/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/sliding/main.nf b/modules/nf-core/seqkit/sliding/main.nf
index 8eaa0fc075b..a20c34e52d5 100644
--- a/modules/nf-core/seqkit/sliding/main.nf
+++ b/modules/nf-core/seqkit/sliding/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_SLIDING {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastx)
diff --git a/modules/nf-core/seqkit/sliding/tests/main.nf.test.snap b/modules/nf-core/seqkit/sliding/tests/main.nf.test.snap
index bceca756d29..204803b7f1b 100644
--- a/modules/nf-core/seqkit/sliding/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/sliding/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,57637a9043c17a7c4b7b3123e07bfe34"
+                    "versions.yml:md5,3e991b964feeae99fc583172952f0975"
                 ],
                 "fastx": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,57637a9043c17a7c4b7b3123e07bfe34"
+                    "versions.yml:md5,3e991b964feeae99fc583172952f0975"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:33:31.037028103"
+        "timestamp": "2025-01-15T15:14:26.642647"
     },
     "sarscov2 - fasta": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,57637a9043c17a7c4b7b3123e07bfe34"
+                    "versions.yml:md5,3e991b964feeae99fc583172952f0975"
                 ],
                 "fastx": [
                     [
@@ -55,15 +55,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,57637a9043c17a7c4b7b3123e07bfe34"
+                    "versions.yml:md5,3e991b964feeae99fc583172952f0975"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:33:12.639274892"
+        "timestamp": "2025-01-15T15:14:18.161346"
     },
     "sarscov2 - fastq": {
         "content": [
@@ -77,7 +77,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,57637a9043c17a7c4b7b3123e07bfe34"
+                    "versions.yml:md5,3e991b964feeae99fc583172952f0975"
                 ],
                 "fastx": [
                     [
@@ -88,14 +88,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,57637a9043c17a7c4b7b3123e07bfe34"
+                    "versions.yml:md5,3e991b964feeae99fc583172952f0975"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:33:21.481895924"
+        "timestamp": "2025-01-15T15:14:22.596449"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/sort/environment.yml b/modules/nf-core/seqkit/sort/environment.yml
index 4f8058a9a57..160a67c08e8 100644
--- a/modules/nf-core/seqkit/sort/environment.yml
+++ b/modules/nf-core/seqkit/sort/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::seqkit=2.8.1"
+  - "bioconda::seqkit=2.9.0"
diff --git a/modules/nf-core/seqkit/sort/main.nf b/modules/nf-core/seqkit/sort/main.nf
index c12e35acc25..19f5a1a47ac 100644
--- a/modules/nf-core/seqkit/sort/main.nf
+++ b/modules/nf-core/seqkit/sort/main.nf
@@ -5,8 +5,8 @@ process SEQKIT_SORT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastx)
diff --git a/modules/nf-core/seqkit/sort/tests/main.nf.test.snap b/modules/nf-core/seqkit/sort/tests/main.nf.test.snap
index 4d3a862b709..6f4de0ff5ba 100644
--- a/modules/nf-core/seqkit/sort/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/sort/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,04ac93fea9e0019536cfe1445ef15472"
+                    "versions.yml:md5,c6f71fc11c6a488880e4afcc5fc166cc"
                 ],
                 "fastx": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,04ac93fea9e0019536cfe1445ef15472"
+                    "versions.yml:md5,c6f71fc11c6a488880e4afcc5fc166cc"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:15:12.840547526"
+        "timestamp": "2025-01-15T15:15:37.898144"
     },
     "sarscov2-test_1_fastq_gz": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,04ac93fea9e0019536cfe1445ef15472"
+                    "versions.yml:md5,c6f71fc11c6a488880e4afcc5fc166cc"
                 ],
                 "fastx": [
                     [
@@ -55,15 +55,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,04ac93fea9e0019536cfe1445ef15472"
+                    "versions.yml:md5,c6f71fc11c6a488880e4afcc5fc166cc"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:14:53.190928013"
+        "timestamp": "2025-01-15T15:15:30.547117"
     },
     "sarscov2-genome_fasta": {
         "content": [
@@ -77,7 +77,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,04ac93fea9e0019536cfe1445ef15472"
+                    "versions.yml:md5,c6f71fc11c6a488880e4afcc5fc166cc"
                 ],
                 "fastx": [
                     [
@@ -88,15 +88,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,04ac93fea9e0019536cfe1445ef15472"
+                    "versions.yml:md5,c6f71fc11c6a488880e4afcc5fc166cc"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:14:29.745582222"
+        "timestamp": "2025-01-15T15:15:21.999443"
     },
     "sarscov2-genome_fasta_gz": {
         "content": [
@@ -110,7 +110,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,04ac93fea9e0019536cfe1445ef15472"
+                    "versions.yml:md5,c6f71fc11c6a488880e4afcc5fc166cc"
                 ],
                 "fastx": [
                     [
@@ -121,14 +121,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,04ac93fea9e0019536cfe1445ef15472"
+                    "versions.yml:md5,c6f71fc11c6a488880e4afcc5fc166cc"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:14:41.460601093"
+        "timestamp": "2025-01-15T15:15:26.228479"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/split2/environment.yml b/modules/nf-core/seqkit/split2/environment.yml
index 41f3e7de43d..1f93892f485 100644
--- a/modules/nf-core/seqkit/split2/environment.yml
+++ b/modules/nf-core/seqkit/split2/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf
index 7a230cd2eb1..b07adaa951c 100644
--- a/modules/nf-core/seqkit/split2/main.nf
+++ b/modules/nf-core/seqkit/split2/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_SPLIT2 {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0' :
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' :
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -20,7 +20,7 @@ process SEQKIT_SPLIT2 {
     script:
     def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if(meta.single_end){
+    if (meta.single_end) {
         """
         seqkit \\
             split2 \\
@@ -50,4 +50,29 @@ process SEQKIT_SPLIT2 {
         END_VERSIONS
         """
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (meta.single_end) {
+        """
+        mkdir -p ${prefix}
+        echo "" | gzip > ${prefix}/${reads[0]}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+        END_VERSIONS
+        """
+    } else {
+        """
+        mkdir -p ${prefix}
+        echo "" | gzip > ${prefix}/${reads[0]}
+        echo "" | gzip > ${prefix}/${reads[1]}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+        END_VERSIONS
+        """
+    }
 }
diff --git a/modules/nf-core/seqkit/split2/meta.yml b/modules/nf-core/seqkit/split2/meta.yml
index c1e6e3def2e..e73024e7dea 100644
--- a/modules/nf-core/seqkit/split2/meta.yml
+++ b/modules/nf-core/seqkit/split2/meta.yml
@@ -41,5 +41,7 @@ output:
           pattern: "versions.yml"
 authors:
   - "@FriederikeHanssen"
+  - "@heuermh"
 maintainers:
   - "@FriederikeHanssen"
+  - "@heuermh"
diff --git a/modules/nf-core/seqkit/split2/tests/main.nf.test.snap b/modules/nf-core/seqkit/split2/tests/main.nf.test.snap
index 071e358541a..2ed2c16570d 100644
--- a/modules/nf-core/seqkit/split2/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/split2/tests/main.nf.test.snap
@@ -17,7 +17,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ],
                 "reads": [
                     [
@@ -34,15 +34,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:49:27.111190403"
+        "timestamp": "2025-01-15T16:15:20.968231"
     },
     "single_end - size": {
         "content": [
@@ -60,7 +60,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ],
                 "reads": [
                     [
@@ -75,15 +75,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:43:42.879258276"
+        "timestamp": "2025-01-15T16:15:16.296246"
     },
     "single_end - part": {
         "content": [
@@ -102,7 +102,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ],
                 "reads": [
                     [
@@ -118,15 +118,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:43:16.85414188"
+        "timestamp": "2025-01-15T16:15:02.927768"
     },
     "single_end - length": {
         "content": [
@@ -144,7 +144,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ],
                 "reads": [
                     [
@@ -159,15 +159,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:42:47.553659985"
+        "timestamp": "2025-01-15T16:14:49.713576"
     },
     "single_end - size - stub": {
         "content": [
@@ -178,14 +178,11 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test_1.part_001.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
-                            "test_1.part_002.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411"
-                        ]
+                        "test_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ],
                 "reads": [
                     [
@@ -193,22 +190,19 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test_1.part_001.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
-                            "test_1.part_002.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411"
-                        ]
+                        "test_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:44:01.29740288"
+        "timestamp": "2025-01-15T16:15:25.267006"
     },
     "single_end - part - stub": {
         "content": [
@@ -219,15 +213,11 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
-                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
-                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52"
-                        ]
+                        "test_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ],
                 "reads": [
                     [
@@ -235,46 +225,19 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
-                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
-                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52"
-                        ]
+                        "test_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:43:33.964460368"
-    },
-    "paired_end - length - stub": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "reads": [
-                    
-                ],
-                "versions": [
-                    
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-05-08T05:42:57.687195505"
+        "timestamp": "2025-01-15T16:15:11.624135"
     },
     "single_end - length - stub": {
         "content": [
@@ -285,14 +248,11 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
-                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d"
-                        ]
+                        "test_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ],
                 "reads": [
                     [
@@ -300,24 +260,21 @@
                             "id": "test",
                             "single_end": true
                         },
-                        [
-                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
-                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d"
-                        ]
+                        "test_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:43:07.15316163"
+        "timestamp": "2025-01-15T16:14:58.47365"
     },
-    "paired_end - part": {
+    "paired_end - length": {
         "content": [
             {
                 "0": [
@@ -327,17 +284,15 @@
                             "single_end": false
                         },
                         [
-                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
-                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
-                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52",
-                            "test_2.part_001.fastq.gz:md5,13d14d69744bd93c8c51873b529bf714",
-                            "test_2.part_002.fastq.gz:md5,5f5a78d78f312164a1159c62d65c15f1",
-                            "test_2.part_003.fastq.gz:md5,48bcbceb485b73bcf1f198e252b016d8"
+                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
+                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d",
+                            "test_2.part_001.fastq.gz:md5,77b9076f82a762711582584342bde5a1",
+                            "test_2.part_002.fastq.gz:md5,33bb6e3edc759baa7ba6580da36def48"
                         ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ],
                 "reads": [
                     [
@@ -346,27 +301,25 @@
                             "single_end": false
                         },
                         [
-                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
-                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
-                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52",
-                            "test_2.part_001.fastq.gz:md5,13d14d69744bd93c8c51873b529bf714",
-                            "test_2.part_002.fastq.gz:md5,5f5a78d78f312164a1159c62d65c15f1",
-                            "test_2.part_003.fastq.gz:md5,48bcbceb485b73bcf1f198e252b016d8"
+                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
+                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d",
+                            "test_2.part_001.fastq.gz:md5,77b9076f82a762711582584342bde5a1",
+                            "test_2.part_002.fastq.gz:md5,33bb6e3edc759baa7ba6580da36def48"
                         ]
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:48:43.715062381"
+        "timestamp": "2025-01-15T16:14:54.230006"
     },
-    "paired_end - length": {
+    "paired_end - part": {
         "content": [
             {
                 "0": [
@@ -376,15 +329,17 @@
                             "single_end": false
                         },
                         [
-                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
-                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d",
-                            "test_2.part_001.fastq.gz:md5,77b9076f82a762711582584342bde5a1",
-                            "test_2.part_002.fastq.gz:md5,33bb6e3edc759baa7ba6580da36def48"
+                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
+                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
+                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52",
+                            "test_2.part_001.fastq.gz:md5,13d14d69744bd93c8c51873b529bf714",
+                            "test_2.part_002.fastq.gz:md5,5f5a78d78f312164a1159c62d65c15f1",
+                            "test_2.part_003.fastq.gz:md5,48bcbceb485b73bcf1f198e252b016d8"
                         ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ],
                 "reads": [
                     [
@@ -393,22 +348,24 @@
                             "single_end": false
                         },
                         [
-                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
-                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d",
-                            "test_2.part_001.fastq.gz:md5,77b9076f82a762711582584342bde5a1",
-                            "test_2.part_002.fastq.gz:md5,33bb6e3edc759baa7ba6580da36def48"
+                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
+                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
+                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52",
+                            "test_2.part_001.fastq.gz:md5,13d14d69744bd93c8c51873b529bf714",
+                            "test_2.part_002.fastq.gz:md5,5f5a78d78f312164a1159c62d65c15f1",
+                            "test_2.part_003.fastq.gz:md5,48bcbceb485b73bcf1f198e252b016d8"
                         ]
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                    "versions.yml:md5,f5d878e7143d05609ce5bb5974126990"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T05:46:21.786837526"
+        "timestamp": "2025-01-15T16:15:07.43572"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/stats/environment.yml b/modules/nf-core/seqkit/stats/environment.yml
index 41f3e7de43d..1f93892f485 100644
--- a/modules/nf-core/seqkit/stats/environment.yml
+++ b/modules/nf-core/seqkit/stats/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/stats/main.nf b/modules/nf-core/seqkit/stats/main.nf
index 117c6052b83..57d95cfdc06 100644
--- a/modules/nf-core/seqkit/stats/main.nf
+++ b/modules/nf-core/seqkit/stats/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_STATS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0' :
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' :
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -31,4 +31,15 @@ process SEQKIT_STATS {
         seqkit: \$( seqkit version | sed 's/seqkit v//' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$( seqkit version | sed 's/seqkit v//' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/seqkit/stats/meta.yml b/modules/nf-core/seqkit/stats/meta.yml
index 797712b5bb9..418aa81e902 100644
--- a/modules/nf-core/seqkit/stats/meta.yml
+++ b/modules/nf-core/seqkit/stats/meta.yml
@@ -44,5 +44,7 @@ output:
           pattern: "versions.yml"
 authors:
   - "@Midnighter"
+  - "@heuermh"
 maintainers:
   - "@Midnighter"
+  - "@heuermh"
diff --git a/modules/nf-core/seqkit/stats/tests/main.nf.test.snap b/modules/nf-core/seqkit/stats/tests/main.nf.test.snap
index 43aa9fe2a72..6ce591131fb 100644
--- a/modules/nf-core/seqkit/stats/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/stats/tests/main.nf.test.snap
@@ -8,11 +8,11 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.tsv:md5,49ea41204974d82fb9bbb30572485ccb"
+                        "test.tsv:md5,14f97a9e0414998854ead651e0e69449"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ],
                 "stats": [
                     [
@@ -20,19 +20,19 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.tsv:md5,49ea41204974d82fb9bbb30572485ccb"
+                        "test.tsv:md5,14f97a9e0414998854ead651e0e69449"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:35:18.621881722"
+        "timestamp": "2025-01-15T15:35:09.132477"
     },
     "genome_fasta": {
         "content": [
@@ -43,11 +43,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.tsv:md5,af2521fa0c7e1a0683e60df6292429de"
+                        "test.tsv:md5,82b33df8ec2515560b80c3d0bc64c898"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ],
                 "stats": [
                     [
@@ -55,19 +55,19 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.tsv:md5,af2521fa0c7e1a0683e60df6292429de"
+                        "test.tsv:md5,82b33df8ec2515560b80c3d0bc64c898"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:35:28.193047869"
+        "timestamp": "2025-01-15T15:35:13.678978"
     },
     "transcriptome_fasta": {
         "content": [
@@ -78,11 +78,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.tsv:md5,48d5664c3214880f3509226cb839eb17"
+                        "test.tsv:md5,eef67c2e2f225391836d59d5b0d6c3b7"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ],
                 "stats": [
                     [
@@ -90,19 +90,19 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.tsv:md5,48d5664c3214880f3509226cb839eb17"
+                        "test.tsv:md5,eef67c2e2f225391836d59d5b0d6c3b7"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:35:39.129387891"
+        "timestamp": "2025-01-15T15:35:18.204844"
     },
     "single_end": {
         "content": [
@@ -113,11 +113,11 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.tsv:md5,97eb700f7e607dba8371e82d5de8a1a2"
+                        "test.tsv:md5,f172827a8608b646559cc39c6ca05085"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ],
                 "stats": [
                     [
@@ -125,19 +125,19 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.tsv:md5,97eb700f7e607dba8371e82d5de8a1a2"
+                        "test.tsv:md5,f172827a8608b646559cc39c6ca05085"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:34:57.889856349"
+        "timestamp": "2025-01-15T15:35:00.240123"
     },
     "paired_end": {
         "content": [
@@ -148,11 +148,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.tsv:md5,97eb700f7e607dba8371e82d5de8a1a2"
+                        "test.tsv:md5,f172827a8608b646559cc39c6ca05085"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ],
                 "stats": [
                     [
@@ -160,19 +160,19 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.tsv:md5,97eb700f7e607dba8371e82d5de8a1a2"
+                        "test.tsv:md5,f172827a8608b646559cc39c6ca05085"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:35:09.114729727"
+        "timestamp": "2025-01-15T15:35:04.668822"
     },
     "single_end - stub": {
         "content": [
@@ -183,11 +183,11 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.tsv:md5,97eb700f7e607dba8371e82d5de8a1a2"
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ],
                 "stats": [
                     [
@@ -195,18 +195,18 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.tsv:md5,97eb700f7e607dba8371e82d5de8a1a2"
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e5810dac4e10040b1a74b8672a829734"
+                    "versions.yml:md5,40bf07b7fd9e00784395ff7746ec8492"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:35:49.267660809"
+        "timestamp": "2025-01-15T15:35:22.85489"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/translate/environment.yml b/modules/nf-core/seqkit/translate/environment.yml
index 95584e3c48b..f917ae67580 100644
--- a/modules/nf-core/seqkit/translate/environment.yml
+++ b/modules/nf-core/seqkit/translate/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::seqkit=2.8.2"
+  - "bioconda::seqkit=2.9.0"
diff --git a/modules/nf-core/seqkit/translate/main.nf b/modules/nf-core/seqkit/translate/main.nf
index 2b6a60634f2..12e8c4a811f 100644
--- a/modules/nf-core/seqkit/translate/main.nf
+++ b/modules/nf-core/seqkit/translate/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_TRANSLATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.2--h9ee0642_1':
-        'biocontainers/seqkit:2.8.2--h9ee0642_1' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastx)
diff --git a/modules/nf-core/seqkit/translate/tests/main.nf.test.snap b/modules/nf-core/seqkit/translate/tests/main.nf.test.snap
index 68a27185c5f..4d9609137d1 100644
--- a/modules/nf-core/seqkit/translate/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/translate/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ],
                 "fastx": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-09-27T14:11:33.440888698"
+        "timestamp": "2025-01-15T15:20:41.567935"
     },
     "sarscov2 - bam - stub": {
         "content": [
@@ -45,7 +45,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ],
                 "fastx": [
                     [
@@ -57,15 +57,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-09-20T15:24:19.344543763"
+        "timestamp": "2025-01-15T15:20:58.701122"
     },
     "sarscov2-genome_fasta-stub": {
         "content": [
@@ -79,7 +79,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ],
                 "fastx": [
                     [
@@ -90,15 +90,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-09-27T13:58:35.061712261"
+        "timestamp": "2025-01-15T15:21:05.989858"
     },
     "sarscov2 - transcriptome_fasta": {
         "content": [
@@ -112,7 +112,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ],
                 "fastx": [
                     [
@@ -123,15 +123,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-09-27T14:12:02.993246822"
+        "timestamp": "2025-01-15T15:20:54.543009"
     },
     "sarscov2 - genome_fasta_gz": {
         "content": [
@@ -145,7 +145,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ],
                 "fastx": [
                     [
@@ -156,15 +156,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-09-27T14:11:43.884810694"
+        "timestamp": "2025-01-15T15:20:45.963348"
     },
     "sarscov2 - test_1_fastq_gz": {
         "content": [
@@ -178,7 +178,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ],
                 "fastx": [
                     [
@@ -189,14 +189,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,bf64d8d652a9b313153c953eab761f33"
+                    "versions.yml:md5,b69861a1b516ab124aa52e238ef3755c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-09-27T14:11:53.792592007"
+        "timestamp": "2025-01-15T15:20:50.35833"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fasta_explore_search_plot_tidk/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_explore_search_plot_tidk/tests/main.nf.test.snap
index 40bd469c624..7a69a7e67b7 100644
--- a/subworkflows/nf-core/fasta_explore_search_plot_tidk/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fasta_explore_search_plot_tidk/tests/main.nf.test.snap
@@ -56,11 +56,11 @@
                 ],
                 "5": [
                     "versions.yml:md5,02d48eb43c3882d9832c88b9e080b420",
+                    "versions.yml:md5,0864338873810e18c736c9c4d3429cd5",
+                    "versions.yml:md5,5d37588f1ce7605624b2a9b52ff72d0c",
                     "versions.yml:md5,5f9958ea613eceae4b09bb42ecaac656",
                     "versions.yml:md5,6713d71b01fe0402e5d32f1a5a181e0f",
-                    "versions.yml:md5,702fdfb5f74070b208b10384021f3f28",
                     "versions.yml:md5,83a6abbf9b68ec1e6152c5b6eb12f0d7",
-                    "versions.yml:md5,95dde1750b4171bedad83c5340cc712b",
                     "versions.yml:md5,b900c2a21c17ac2d16e33641e64fc7c1"
                 ],
                 "aposteriori_sequence": [
@@ -117,20 +117,20 @@
                 ],
                 "versions": [
                     "versions.yml:md5,02d48eb43c3882d9832c88b9e080b420",
+                    "versions.yml:md5,0864338873810e18c736c9c4d3429cd5",
+                    "versions.yml:md5,5d37588f1ce7605624b2a9b52ff72d0c",
                     "versions.yml:md5,5f9958ea613eceae4b09bb42ecaac656",
                     "versions.yml:md5,6713d71b01fe0402e5d32f1a5a181e0f",
-                    "versions.yml:md5,702fdfb5f74070b208b10384021f3f28",
                     "versions.yml:md5,83a6abbf9b68ec1e6152c5b6eb12f0d7",
-                    "versions.yml:md5,95dde1750b4171bedad83c5340cc712b",
                     "versions.yml:md5,b900c2a21c17ac2d16e33641e64fc7c1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:52:52.0126754"
+        "timestamp": "2025-01-16T07:01:58.803379"
     },
     "homo_sapiens-genome_fasta-genome_21_fasta-no_apriori-stub": {
         "content": [
@@ -185,10 +185,10 @@
                 ],
                 "5": [
                     "versions.yml:md5,02d48eb43c3882d9832c88b9e080b420",
+                    "versions.yml:md5,0864338873810e18c736c9c4d3429cd5",
+                    "versions.yml:md5,5d37588f1ce7605624b2a9b52ff72d0c",
                     "versions.yml:md5,5f9958ea613eceae4b09bb42ecaac656",
-                    "versions.yml:md5,6713d71b01fe0402e5d32f1a5a181e0f",
-                    "versions.yml:md5,702fdfb5f74070b208b10384021f3f28",
-                    "versions.yml:md5,95dde1750b4171bedad83c5340cc712b"
+                    "versions.yml:md5,6713d71b01fe0402e5d32f1a5a181e0f"
                 ],
                 "aposteriori_sequence": [
                     [
@@ -240,18 +240,18 @@
                 ],
                 "versions": [
                     "versions.yml:md5,02d48eb43c3882d9832c88b9e080b420",
+                    "versions.yml:md5,0864338873810e18c736c9c4d3429cd5",
+                    "versions.yml:md5,5d37588f1ce7605624b2a9b52ff72d0c",
                     "versions.yml:md5,5f9958ea613eceae4b09bb42ecaac656",
-                    "versions.yml:md5,6713d71b01fe0402e5d32f1a5a181e0f",
-                    "versions.yml:md5,702fdfb5f74070b208b10384021f3f28",
-                    "versions.yml:md5,95dde1750b4171bedad83c5340cc712b"
+                    "versions.yml:md5,6713d71b01fe0402e5d32f1a5a181e0f"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:53:21.817193592"
+        "timestamp": "2025-01-16T07:02:21.256708"
     },
     "homo_sapiens-genome_fasta-genome_21_fasta-partial_apriori-stub": {
         "content": [
@@ -316,11 +316,11 @@
                 ],
                 "5": [
                     "versions.yml:md5,02d48eb43c3882d9832c88b9e080b420",
+                    "versions.yml:md5,0864338873810e18c736c9c4d3429cd5",
+                    "versions.yml:md5,5d37588f1ce7605624b2a9b52ff72d0c",
                     "versions.yml:md5,5f9958ea613eceae4b09bb42ecaac656",
                     "versions.yml:md5,6713d71b01fe0402e5d32f1a5a181e0f",
-                    "versions.yml:md5,702fdfb5f74070b208b10384021f3f28",
                     "versions.yml:md5,83a6abbf9b68ec1e6152c5b6eb12f0d7",
-                    "versions.yml:md5,95dde1750b4171bedad83c5340cc712b",
                     "versions.yml:md5,b900c2a21c17ac2d16e33641e64fc7c1"
                 ],
                 "aposteriori_sequence": [
@@ -383,19 +383,19 @@
                 ],
                 "versions": [
                     "versions.yml:md5,02d48eb43c3882d9832c88b9e080b420",
+                    "versions.yml:md5,0864338873810e18c736c9c4d3429cd5",
+                    "versions.yml:md5,5d37588f1ce7605624b2a9b52ff72d0c",
                     "versions.yml:md5,5f9958ea613eceae4b09bb42ecaac656",
                     "versions.yml:md5,6713d71b01fe0402e5d32f1a5a181e0f",
-                    "versions.yml:md5,702fdfb5f74070b208b10384021f3f28",
                     "versions.yml:md5,83a6abbf9b68ec1e6152c5b6eb12f0d7",
-                    "versions.yml:md5,95dde1750b4171bedad83c5340cc712b",
                     "versions.yml:md5,b900c2a21c17ac2d16e33641e64fc7c1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:53:07.119615485"
+        "timestamp": "2025-01-16T07:02:10.532406"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test.snap
index c48df3d7ed9..f586e0282fa 100644
--- a/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test.snap
@@ -3,9 +3,9 @@
         "content": [
             [
                 "versions.yml:md5,10138b74aed5b2658c26ddf80ff391d5",
-                "versions.yml:md5,631c0428c28d5355f0e3e9bd790bd77d",
-                "versions.yml:md5,706a3f609ec9d66162576d93a6f6a67b",
-                "versions.yml:md5,756eee52b4a45f7a9effe33b1cd3cb92"
+                "versions.yml:md5,756eee52b4a45f7a9effe33b1cd3cb92",
+                "versions.yml:md5,9a9fc91d495845c5c9b456d55390da95",
+                "versions.yml:md5,e7bce91addb97e0d2f5ca1869adeeed4"
             ],
             true,
             "result_small_Clone1_N1.bed:md5,98a74ac6dd16ee876e9a3f54d2695c88",