diff --git a/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test b/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test
new file mode 100644
index 00000000000..e0396a63cac
--- /dev/null
+++ b/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test
@@ -0,0 +1,36 @@
+
+nextflow_process {
+
+    name "Test Process UCSC_GTFTOGENEPRED"
+    script "../main.nf"
+    process "UCSC_GTFTOGENEPRED"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ucsc"
+    tag "ucsc/gtftogenepred"
+
+    test("test-ucsc-gtftogenepred") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id: 'test' ], // meta map
+				    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test.snap b/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test.snap
new file mode 100644
index 00000000000..f021f823805
--- /dev/null
+++ b/modules/nf-core/ucsc/gtftogenepred/tests/main.nf.test.snap
@@ -0,0 +1,51 @@
+{
+    "test-ucsc-gtftogenepred": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.genepred:md5,779e4749efaf38da3443ddfde30cc76c"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.refflat:md5,4101802f41d4cf7ee2667587da11bf42"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,fd95365619a316eb451190365b1b799e"
+                ],
+                "genepred": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.genepred:md5,779e4749efaf38da3443ddfde30cc76c"
+                    ]
+                ],
+                "refflat": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.refflat:md5,4101802f41d4cf7ee2667587da11bf42"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,fd95365619a316eb451190365b1b799e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T08:55:50.58172"
+    }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/ucsc/gtftogenepred/nextflow.config b/modules/nf-core/ucsc/gtftogenepred/tests/nextflow.config
similarity index 59%
rename from tests/modules/nf-core/ucsc/gtftogenepred/nextflow.config
rename to modules/nf-core/ucsc/gtftogenepred/tests/nextflow.config
index dd4e776cfd8..889bb6ce65c 100644
--- a/tests/modules/nf-core/ucsc/gtftogenepred/nextflow.config
+++ b/modules/nf-core/ucsc/gtftogenepred/tests/nextflow.config
@@ -1,7 +1,4 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: UCSC_GTFTOGENEPRED {
         ext.args = [
             "-genePredExt",
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 476c1a5de98..01bc2333264 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1539,9 +1539,6 @@ truvari/bench:
 ucsc/bedtobigbed:
   - modules/nf-core/ucsc/bedtobigbed/**
   - tests/modules/nf-core/ucsc/bedtobigbed/**
-ucsc/gtftogenepred:
-  - modules/nf-core/ucsc/gtftogenepred/**
-  - tests/modules/nf-core/ucsc/gtftogenepred/**
 ucsc/wigtobigwig:
   - modules/nf-core/ucsc/wigtobigwig/**
   - tests/modules/nf-core/ucsc/wigtobigwig/**
diff --git a/tests/modules/nf-core/ucsc/gtftogenepred/main.nf b/tests/modules/nf-core/ucsc/gtftogenepred/main.nf
deleted file mode 100644
index 60dc96eeb88..00000000000
--- a/tests/modules/nf-core/ucsc/gtftogenepred/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UCSC_GTFTOGENEPRED } from '../../../../../modules/nf-core/ucsc/gtftogenepred/main.nf'
-
-workflow test_ucsc_gtftogenepred {
-
-    input = [
-        [ id: 'test' ], // meta map
-        [ file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true ) ]
-    ]
-
-    UCSC_GTFTOGENEPRED ( input )
-}
diff --git a/tests/modules/nf-core/ucsc/gtftogenepred/test.yml b/tests/modules/nf-core/ucsc/gtftogenepred/test.yml
deleted file mode 100644
index 08fcffa56e4..00000000000
--- a/tests/modules/nf-core/ucsc/gtftogenepred/test.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-- name: ucsc gtftogenepred test_ucsc_gtftogenepred
-  command: nextflow run ./tests/modules/nf-core/ucsc/gtftogenepred -entry test_ucsc_gtftogenepred -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ucsc/gtftogenepred/nextflow.config
-  tags:
-    - ucsc/gtftogenepred
-    - ucsc
-  files:
-    - path: output/ucsc/test.genepred
-      md5sum: 779e4749efaf38da3443ddfde30cc76c
-    - path: output/ucsc/test.refflat
-      md5sum: 4101802f41d4cf7ee2667587da11bf42
-    - path: output/ucsc/versions.yml