diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test b/modules/nf-core/kraken2/kraken2/tests/main.nf.test
index c0843df29acf..40f471e66504 100644
--- a/modules/nf-core/kraken2/kraken2/tests/main.nf.test
+++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test
@@ -133,10 +133,80 @@ nextflow_process {
             { assert process.success },
             { assert snapshot(
                     process.out.report,
+                    process.out.versions,
                     process.out.classified_reads_assignment,
+                ).match()
+            },
+            )
+        }
+    }
+
+    test("single_end - stub") {
+
+    tag "stub"
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    [ file("dummy1", checkIfExists: false)]
+                ]
+                input[1] = file("dummy2", checkIfExists: false)
+                input[2] = true
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(
+                    process.out.report,
+                    process.out.versions,
+                ).match()
+            },
+            { assert process.out.classified_reads_fastq.get(0).get(1) ==~ ".*/test.classified.fastq.gz" },
+            { assert process.out.unclassified_reads_fastq.get(0).get(1) ==~ ".*/test.unclassified.fastq.gz" },
+            )
+        }
+    }
+
+    test("paired_end - stub") {
+
+    tag "stub"
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [ file("dummy1", checkIfExists: false)]
+                ]
+                input[1] = file("dummy2", checkIfExists: false)
+                input[2] = true
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(
+                    process.out.report,
                     process.out.versions,
                 ).match()
             },
+            { assert process.out.classified_reads_fastq.get(0).get(1).get(0)
+                ==~ ".*/test.classified_1.fastq.gz" },
+            { assert process.out.classified_reads_fastq.get(0).get(1).get(1)
+                ==~ ".*/test.classified_2.fastq.gz" },
+            { assert process.out.unclassified_reads_fastq.get(0).get(1).get(0)
+                ==~ ".*/test.unclassified_1.fastq.gz" },
+            { assert process.out.unclassified_reads_fastq.get(0).get(1).get(1)
+                ==~ ".*/test.unclassified_2.fastq.gz" },
             )
         }
     }
diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap b/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap
index eb062ed1e596..defe4e24df31 100644
--- a/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap
+++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap
@@ -15,10 +15,55 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-29T10:39:33.16840511"
+    },
+    "paired_end - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.kraken2.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                "versions.yml:md5,3f1efbca96594bcbd7759bd992f3ffda"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-29T10:57:46.285333986"
+    },
+    "sarscov2 custom_prefix - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.kraken2.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,79adf2ca1cfc625cb77e391b27142c43"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-09-26T10:40:05.762965901"
+        "timestamp": "2025-10-16T13:56:24.287200136"
     },
     "sarscov2 illumina paired end [fastq]": {
         "content": [
@@ -52,6 +97,9 @@
                     "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e"
                 ]
             ],
+            [
+                "versions.yml:md5,3f1efbca96594bcbd7759bd992f3ffda"
+            ],
             [
                 [
                     {
@@ -60,15 +108,33 @@
                     },
                     "test.kraken2.classifiedreads.txt:md5,e7a90531f0d8d777316515c36fe4cae0"
                 ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-11-04T16:53:38.496195464"
+    },
+    "single_end - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.kraken2.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
             ],
             [
                 "versions.yml:md5,3f1efbca96594bcbd7759bd992f3ffda"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-09-26T10:40:19.91998338"
+        "timestamp": "2025-10-29T10:44:44.698158761"
     }
 }
\ No newline at end of file