diff --git a/modules/nf-core/mmseqs/databases/tests/main.nf.test b/modules/nf-core/mmseqs/databases/tests/main.nf.test
new file mode 100644
index 000000000000..fdb7ef9ff076
--- /dev/null
+++ b/modules/nf-core/mmseqs/databases/tests/main.nf.test
@@ -0,0 +1,51 @@
+
+nextflow_process {
+
+    name "Test Process MMSEQS_DATABASES"
+    script "../main.nf"
+    process "MMSEQS_DATABASES"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "mmseqs"
+    tag "mmseqs/databases"
+
+    test("test-mmseqs-databases") {
+        
+        when {
+            process {
+                """
+                input[0] = "SILVA"
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+    
+    test("test-mmseqs-databases-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = "SILVA"
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+    
+}
diff --git a/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap b/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap
new file mode 100644
index 000000000000..a28e6eecfdd7
--- /dev/null
+++ b/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap
@@ -0,0 +1,96 @@
+{
+    "test-mmseqs-databases": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "database:md5,1c0ce0899156843604869205a1fdebf7",
+                        "database.dbtype:md5,c8ed20c23ba91f4577f84c940c86c7db",
+                        "database.index:md5,19128cfcc6d0fa5dd7451938e8e7481f",
+                        "database.lookup:md5,03cb3ae6b0580a858ddf5fd5eb1e4cab",
+                        "database.source:md5,acf29bfb5e2a3febe53a3349d778cacd",
+                        "database.version:md5,03643ccd1930642c55e3cfca40a7309f",
+                        "database_h:md5,8931d1d093e2332a134ec5f2b6c12ca4",
+                        "database_h.dbtype:md5,8895d3d8e9322aedbf45249dfb3ddb0a",
+                        "database_h.index:md5,976c04c17837a4ba64ec119588339f14",
+                        "database_mapping:md5,712219037a5f289aa210c0681e4dc82f",
+                        "database_taxonomy:md5,b3d9d456534c691fdd3e158887892bab"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b038db45e5934b8f0f743449bbac01b4"
+                ],
+                "database": [
+                    [
+                        "database:md5,1c0ce0899156843604869205a1fdebf7",
+                        "database.dbtype:md5,c8ed20c23ba91f4577f84c940c86c7db",
+                        "database.index:md5,19128cfcc6d0fa5dd7451938e8e7481f",
+                        "database.lookup:md5,03cb3ae6b0580a858ddf5fd5eb1e4cab",
+                        "database.source:md5,acf29bfb5e2a3febe53a3349d778cacd",
+                        "database.version:md5,03643ccd1930642c55e3cfca40a7309f",
+                        "database_h:md5,8931d1d093e2332a134ec5f2b6c12ca4",
+                        "database_h.dbtype:md5,8895d3d8e9322aedbf45249dfb3ddb0a",
+                        "database_h.index:md5,976c04c17837a4ba64ec119588339f14",
+                        "database_mapping:md5,712219037a5f289aa210c0681e4dc82f",
+                        "database_taxonomy:md5,b3d9d456534c691fdd3e158887892bab"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b038db45e5934b8f0f743449bbac01b4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T17:00:12.286094"
+    },
+    "test-mmseqs-databases-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "database:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.source:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.version:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_mapping:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,49082428ec974e4ddb09a6ca2e9f21b3"
+                ],
+                "database": [
+                    [
+                        "database:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.source:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database.version:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_mapping:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "database_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,49082428ec974e4ddb09a6ca2e9f21b3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T17:00:20.527628"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index e890d0f68ada..5024703f73c4 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -518,9 +518,6 @@ mitohifi/mitohifi:
 mmseqs/cluster:
   - modules/nf-core/mmseqs/cluster/**
   - tests/modules/nf-core/mmseqs/cluster/**
-mmseqs/databases:
-  - modules/nf-core/mmseqs/databases/**
-  - tests/modules/nf-core/mmseqs/databases/**
 mmseqs/easysearch:
   - modules/nf-core/mmseqs/easysearch/**
   - tests/modules/nf-core/mmseqs/easysearch/**
diff --git a/tests/modules/nf-core/mmseqs/databases/main.nf b/tests/modules/nf-core/mmseqs/databases/main.nf
deleted file mode 100644
index bd0bb9d4eb60..000000000000
--- a/tests/modules/nf-core/mmseqs/databases/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MMSEQS_DATABASES } from '../../../../../modules/nf-core/mmseqs/databases/main.nf'
-
-workflow test_mmseqs_databases {
-
-    input = "SILVA"
-
-    MMSEQS_DATABASES ( input )
-}
diff --git a/tests/modules/nf-core/mmseqs/databases/nextflow.config b/tests/modules/nf-core/mmseqs/databases/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/mmseqs/databases/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/mmseqs/databases/test.yml b/tests/modules/nf-core/mmseqs/databases/test.yml
deleted file mode 100644
index dee34721b304..000000000000
--- a/tests/modules/nf-core/mmseqs/databases/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: mmseqs databases test_mmseqs_databases
-  command: nextflow run ./tests/modules/nf-core/mmseqs/databases -entry test_mmseqs_databases -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mmseqs/databases/nextflow.config
-  tags:
-    - mmseqs
-    - mmseqs/databases
-  files:
-    - path: output/mmseqs/mmseqs_database/database
-    - path: output/mmseqs/mmseqs_database/database.dbtype
-    - path: output/mmseqs/mmseqs_database/database.index
-    - path: output/mmseqs/mmseqs_database/database.lookup
-    - path: output/mmseqs/mmseqs_database/database.source
-    - path: output/mmseqs/mmseqs_database/database.version
-    - path: output/mmseqs/mmseqs_database/database_h
-    - path: output/mmseqs/mmseqs_database/database_h.dbtype
-    - path: output/mmseqs/mmseqs_database/database_h.index
-    - path: output/mmseqs/mmseqs_database/database_mapping
-    - path: output/mmseqs/mmseqs_database/database_taxonomy
-    - path: output/mmseqs/versions.yml