diff --git a/modules/nf-core/rapidnj/tests/main.nf.test b/modules/nf-core/rapidnj/tests/main.nf.test
new file mode 100644
index 00000000000..69b8120cfb5
--- /dev/null
+++ b/modules/nf-core/rapidnj/tests/main.nf.test
@@ -0,0 +1,36 @@
+
+nextflow_process {
+
+    name "Test Process RAPIDNJ"
+    script "../main.nf"
+    process "RAPIDNJ"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "rapidnj"
+
+    test("test-rapidnj") {
+        
+        when {
+            process {
+                """
+                input[0] = [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					process.out.stockholm_alignment,
+					file(process.out.phylogeny[0][1]).name,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+    
+}
diff --git a/modules/nf-core/rapidnj/tests/main.nf.test.snap b/modules/nf-core/rapidnj/tests/main.nf.test.snap
new file mode 100644
index 00000000000..067322f28aa
--- /dev/null
+++ b/modules/nf-core/rapidnj/tests/main.nf.test.snap
@@ -0,0 +1,18 @@
+{
+    "test-rapidnj": {
+        "content": [
+            [
+                "alignment.sth:md5,d2e995c5dd3e3a8212a98414ae5b5de7"
+            ],
+            "U",
+            [
+                "versions.yml:md5,6949732c2fc12b8a5a3e478f197e7fe7"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T10:46:46.856713"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index b698856bbae..48c0c4601c2 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1232,9 +1232,6 @@ qcat:
 quast:
   - modules/nf-core/quast/**
   - tests/modules/nf-core/quast/**
-rapidnj:
-  - modules/nf-core/rapidnj/**
-  - tests/modules/nf-core/rapidnj/**
 raven:
   - modules/nf-core/raven/**
   - tests/modules/nf-core/raven/**
diff --git a/tests/modules/nf-core/rapidnj/main.nf b/tests/modules/nf-core/rapidnj/main.nf
deleted file mode 100644
index af9caac2f95..00000000000
--- a/tests/modules/nf-core/rapidnj/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { RAPIDNJ } from '../../../../modules/nf-core/rapidnj/main.nf'
-
-workflow test_rapidnj {
-    
-    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
-
-    RAPIDNJ ( input )
-}
diff --git a/tests/modules/nf-core/rapidnj/nextflow.config b/tests/modules/nf-core/rapidnj/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/rapidnj/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/rapidnj/test.yml b/tests/modules/nf-core/rapidnj/test.yml
deleted file mode 100644
index 2372aa02154..00000000000
--- a/tests/modules/nf-core/rapidnj/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: rapidnj
-  command: nextflow run ./tests/modules/nf-core/rapidnj -entry test_rapidnj -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rapidnj/nextflow.config
-  tags:
-    - rapidnj
-  files:
-    - path: output/rapidnj/alignment.sth
-      md5sum: d2e995c5dd3e3a8212a98414ae5b5de7
-    - path: output/rapidnj/rapidnj_phylogeny.tre
-      md5sum: 775909ea40138101976592cfa1814a1d