diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test
new file mode 100644
index 000000000000..2891bf9e4b19
--- /dev/null
+++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test
@@ -0,0 +1,72 @@
+nextflow_process {
+
+    name "Test Process GATK4_INTERVALLISTTOOLS"
+    script "../main.nf"
+    process "GATK4_INTERVALLISTTOOLS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/bedtointervallist"
+    tag "gatk4/intervallisttools"
+
+    setup {
+        run("GATK4_BEDTOINTERVALLIST") {
+            script "../../bedtointervallist/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)]
+                ]
+                input[1] = [
+                    [ id:'dict' ], // meta map
+                    [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]
+                ]
+                """
+            }
+        }
+    }
+
+    test("test_gatk4_intervallisttools") {
+
+        when {
+            process {
+                """
+                input[0] = GATK4_BEDTOINTERVALLIST.out.interval_list
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+    test("test_gatk4_intervallisttools -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = GATK4_BEDTOINTERVALLIST.out.interval_list
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap
new file mode 100644
index 000000000000..7718ed003829
--- /dev/null
+++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap
@@ -0,0 +1,88 @@
+{
+    "test_gatk4_intervallisttools": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "1scattered.interval_list:md5,64f6665f9fbd257e4a300ec602f4e995",
+                            "2scattered.interval_list:md5,f515c3da0c6accfd8e7dc33df50855c5",
+                            "3scattered.interval_list:md5,7a918e8c9211b54334587793e8cbae53",
+                            "4scattered.interval_list:md5,1b93105227a7dc81f07101a1efd31498"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03"
+                ],
+                "interval_list": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "1scattered.interval_list:md5,64f6665f9fbd257e4a300ec602f4e995",
+                            "2scattered.interval_list:md5,f515c3da0c6accfd8e7dc33df50855c5",
+                            "3scattered.interval_list:md5,7a918e8c9211b54334587793e8cbae53",
+                            "4scattered.interval_list:md5,1b93105227a7dc81f07101a1efd31498"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.2"
+        },
+        "timestamp": "2024-05-22T21:26:22.252885"
+    },
+    "test_gatk4_intervallisttools -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "1scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "2scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "3scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "4scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03"
+                ],
+                "interval_list": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "1scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "2scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "3scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "4scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.2"
+        },
+        "timestamp": "2024-05-22T22:15:11.772344"
+    }
+}
\ No newline at end of file
diff --git a/tests/modules/nf-core/gatk4/intervallisttools/nextflow.config b/modules/nf-core/gatk4/intervallisttools/tests/nextflow.config
similarity index 64%
rename from tests/modules/nf-core/gatk4/intervallisttools/nextflow.config
rename to modules/nf-core/gatk4/intervallisttools/tests/nextflow.config
index b751ad9bc1db..b24b20db0f22 100644
--- a/tests/modules/nf-core/gatk4/intervallisttools/nextflow.config
+++ b/modules/nf-core/gatk4/intervallisttools/tests/nextflow.config
@@ -1,9 +1,5 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: GATK4_INTERVALLISTTOOLS {
         ext.args = '--SCATTER_COUNT 6 --SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW --UNIQUE true --SORT true'
     }
-
 }
diff --git a/modules/nf-core/gatk4/intervallisttools/tests/tags.yml b/modules/nf-core/gatk4/intervallisttools/tests/tags.yml
new file mode 100644
index 000000000000..bf85ff5fac37
--- /dev/null
+++ b/modules/nf-core/gatk4/intervallisttools/tests/tags.yml
@@ -0,0 +1,2 @@
+gatk4/intervallisttools:
+  - "modules/nf-core/gatk4/intervallisttools/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index c237ed4a13dd..3e7840d1fcd7 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -618,9 +618,6 @@ gatk4/germlinecnvcaller:
 gatk4/intervallisttobed:
   - modules/nf-core/gatk4/intervallisttobed/**
   - tests/modules/nf-core/gatk4/intervallisttobed/**
-gatk4/intervallisttools:
-  - modules/nf-core/gatk4/intervallisttools/**
-  - tests/modules/nf-core/gatk4/intervallisttools/**
 gatk4/learnreadorientationmodel:
   - modules/nf-core/gatk4/learnreadorientationmodel/**
   - tests/modules/nf-core/gatk4/learnreadorientationmodel/**
diff --git a/tests/modules/nf-core/gatk4/intervallisttools/main.nf b/tests/modules/nf-core/gatk4/intervallisttools/main.nf
deleted file mode 100644
index 44b153625148..000000000000
--- a/tests/modules/nf-core/gatk4/intervallisttools/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_BEDTOINTERVALLIST } from '../../../../../modules/nf-core/gatk4/bedtointervallist/main.nf'
-include { GATK4_INTERVALLISTTOOLS } from '../../../../../modules/nf-core/gatk4/intervallisttools/main.nf'
-
-workflow test_gatk4_intervallisttools {
-
-    input = [
-        [ id:'test' ],
-        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    ]
-    dict = Channel.fromPath(file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true))
-        .map{ dict -> [ [id:'test'], dict ] }
-
-    GATK4_BEDTOINTERVALLIST ( input, dict )
-    GATK4_INTERVALLISTTOOLS ( GATK4_BEDTOINTERVALLIST.out.interval_list )
-}
diff --git a/tests/modules/nf-core/gatk4/intervallisttools/test.yml b/tests/modules/nf-core/gatk4/intervallisttools/test.yml
deleted file mode 100644
index 7d326171518e..000000000000
--- a/tests/modules/nf-core/gatk4/intervallisttools/test.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-- name: gatk4 intervallisttools test_gatk4_intervallisttools
-  command: nextflow run ./tests/modules/nf-core/gatk4/intervallisttools -entry test_gatk4_intervallisttools -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/intervallisttools/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/intervallisttools
-  files:
-    - path: output/gatk4/test.interval_list
-      md5sum: e51101c9357fb2d59fd30e370eefa39c
-    - path: output/gatk4/test_split/temp_0001_of_6/1scattered.interval_list
-      md5sum: 64f6665f9fbd257e4a300ec602f4e995
-    - path: output/gatk4/test_split/temp_0002_of_6/2scattered.interval_list
-      md5sum: f515c3da0c6accfd8e7dc33df50855c5
-    - path: output/gatk4/test_split/temp_0003_of_6/3scattered.interval_list
-      md5sum: 7a918e8c9211b54334587793e8cbae53
-    - path: output/gatk4/test_split/temp_0004_of_6/4scattered.interval_list
-      md5sum: 1b93105227a7dc81f07101a1efd31498
-    - path: output/gatk4/versions.yml