diff --git a/modules/nf-core/mygene/main.nf b/modules/nf-core/mygene/main.nf
index 70141d142f80..1d49dc52f75f 100644
--- a/modules/nf-core/mygene/main.nf
+++ b/modules/nf-core/mygene/main.nf
@@ -13,11 +13,23 @@ process MYGENE {
     output:
     tuple val(meta), path("*.gmt"), emit: gmt
     tuple val(meta), path("*.tsv"), emit: tsv     , optional: true
-    path "versions.yml"           , emit: versions
+    path "versions.yml"           , emit: versions_mygene, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     template "mygene.py"
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.gmt
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mygene: \$(python3 -c 'import mygene; print(mygene.__version__)')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/mygene/meta.yml b/modules/nf-core/mygene/meta.yml
index 8356c502ef32..2683c9ee20f9 100644
--- a/modules/nf-core/mygene/meta.yml
+++ b/modules/nf-core/mygene/meta.yml
@@ -11,9 +11,9 @@ tools:
       documentation: "https://docs.mygene.info/projects/mygene-py/en/latest/"
       tool_dev_url: "https://github.com/biothings/mygene.py"
       doi: "10.1093/nar/gks1114"
-      licence: ["Apache-2.0"]
+      licence:
+        - "Apache-2.0"
       identifier: biotools:mygene
-
 input:
   - - meta:
         type: map
@@ -22,9 +22,9 @@ input:
           e.g. `[ id:'sample1' ]`
     - gene_list:
         type: file
-        description: A tsv/csv file that contains a list of gene ids in one of the columns.
-          By default, the column name should be "gene_id", but this can be changed by
-          using "--columname gene_id" in ext.args.
+        description: A tsv/csv file that contains a list of gene ids in one of the
+          columns. By default, the column name should be "gene_id", but this can
+          be changed by using "--columname gene_id" in ext.args.
         pattern: "*.{csv,tsv}"
         ontologies:
           - edam: http://edamontology.org/format_3752 # CSV
@@ -55,14 +55,23 @@ output:
             query, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid
           pattern: "*.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
+
+  versions_mygene:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750
+topics:
   versions:
     - versions.yml:
         type: file
         description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
 authors:
   - "@suzannejin"
 maintainers:
diff --git a/modules/nf-core/mygene/tests/main.nf.test b/modules/nf-core/mygene/tests/main.nf.test
index e5ba64caa3b8..f3b418f44ef6 100644
--- a/modules/nf-core/mygene/tests/main.nf.test
+++ b/modules/nf-core/mygene/tests/main.nf.test
@@ -25,8 +25,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - default options - gmt") },
-                { assert snapshot(process.out.versions).match("mygene - default options - versions") }
+                { assert snapshot(
+                    sanitizeOutput(process.out),
+                    process.out.versions_mygene[0]
+                ).match() }
             )
         }
     }
@@ -49,9 +51,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - default with tsv file - gmt") },
-                { assert snapshot(process.out.tsv).match("mygene - default with tsv file - tsv") },
-                { assert snapshot(process.out.versions).match("mygene - default with tsv file - versions") }
+                { assert snapshot(
+                    sanitizeOutput(process.out),
+                    process.out.versions_mygene[0]
+                ).match() }
             )
         }
     }
@@ -74,8 +77,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - filter by go category - gmt") },
-                { assert snapshot(process.out.versions).match("mygene - filter by go category - versions") }
+                { assert snapshot(
+                    sanitizeOutput(process.out),
+                    process.out.versions_mygene[0]
+                ).match() }
             )
         }
     }
@@ -98,8 +103,35 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.gmt).match("mygene - filter by go evidence - gmt") },
-                { assert snapshot(process.out.versions).match("mygene - filter by go evidence - versions") }
+                { assert snapshot(
+                    sanitizeOutput(process.out),
+                    process.out.versions_mygene[0]
+                ).match() }
+            )
+        }
+    }
+
+    test("mygene - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id : 'test'],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv")
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    sanitizeOutput(process.out),
+                    process.out.versions_mygene[0]
+                ).match() }
             )
         }
     }
diff --git a/modules/nf-core/mygene/tests/main.nf.test.snap b/modules/nf-core/mygene/tests/main.nf.test.snap
index d6a334c7ed62..23a9b58244fd 100644
--- a/modules/nf-core/mygene/tests/main.nf.test.snap
+++ b/modules/nf-core/mygene/tests/main.nf.test.snap
@@ -1,135 +1,142 @@
 {
-    "mygene - filter by go evidence - versions": {
+    "mygene - stub": {
         "content": [
-            [
-                "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:31.854823"
-    },
-    "mygene - default options - versions": {
-        "content": [
-            [
-                "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:19:43.081388"
-    },
-    "mygene - default with tsv file - versions": {
-        "content": [
-            [
-                "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:01.837699"
-    },
-    "mygene - default options - gmt": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gmt:md5,d76d4d06dad199c5e3ecef7060876834"
+            {
+                "gmt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gmt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_mygene": [
+                    "versions.yml:md5,8ed326917ca1d32d3f633a2f0be6a47c"
                 ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:19:43.060437"
-    },
-    "mygene - filter by go category - versions": {
-        "content": [
-            [
-                "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
-            ]
+            },
+            "versions.yml:md5,8ed326917ca1d32d3f633a2f0be6a47c"
         ],
+        "timestamp": "2026-05-01T07:52:01.578258",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:17.233994"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
-    "mygene - filter by go evidence - gmt": {
+    "mygene - default options": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gmt:md5,da6b31a5f889e3aedb16b4154f9652af"
+            {
+                "gmt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gmt:md5,1ab1d063c8ea81d5fa70c1c05ac8eef8"
+                    ]
+                ],
+                "tsv": [
+                    
+                ],
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
-            ]
+            },
+            "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
+        "timestamp": "2026-05-01T07:51:09.551117",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:31.827798"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
-    "mygene - default with tsv file - tsv": {
+    "mygene - filter by go evidence": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.tsv:md5,018e23173b224cbf328751006593900e"
+            {
+                "gmt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gmt:md5,9522f1a93897fb9b1a2b2109cb49baa1"
+                    ]
+                ],
+                "tsv": [
+                    
+                ],
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
-            ]
+            },
+            "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
+        "timestamp": "2026-05-01T07:51:54.816787",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:01.81872"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
-    "mygene - default with tsv file - gmt": {
+    "mygene - filter by go category": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gmt:md5,d76d4d06dad199c5e3ecef7060876834"
+            {
+                "gmt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gmt:md5,369d949e20afdb7a1645c7794a078e8b"
+                    ]
+                ],
+                "tsv": [
+                    
+                ],
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
-            ]
+            },
+            "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
+        "timestamp": "2026-05-01T07:51:41.300263",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:01.79811"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
-    "mygene - filter by go category - gmt": {
+    "mygene - default with tsv file": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gmt:md5,213c1d1d2345df8ea51d67cb1670f4f7"
+            {
+                "gmt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.gmt:md5,1ab1d063c8ea81d5fa70c1c05ac8eef8"
+                    ]
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tsv:md5,3a7e5fe0b8efb0258dcd46326a498eb1"
+                    ]
+                ],
+                "versions_mygene": [
+                    "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
                 ]
-            ]
+            },
+            "versions.yml:md5,09d72645c3ae7e886af6e8bd2876c72b"
         ],
+        "timestamp": "2026-05-01T07:51:27.504956",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-20T17:20:17.208509"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file