diff --git a/modules/nf-core/bedtools/makewindows/tests/main.nf.test b/modules/nf-core/bedtools/makewindows/tests/main.nf.test
new file mode 100644
index 00000000000..b27e59b6e04
--- /dev/null
+++ b/modules/nf-core/bedtools/makewindows/tests/main.nf.test
@@ -0,0 +1,58 @@
+
+nextflow_process {
+
+    name "Test Process BEDTOOLS_MAKEWINDOWS"
+    script "../main.nf"
+    process "BEDTOOLS_MAKEWINDOWS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bedtools"
+    tag "bedtools/makewindows"
+
+    test("test-bedtools-makewindows-bed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test2'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-bedtools-makewindows-fai") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test2'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/bedtools/makewindows/tests/main.nf.test.snap b/modules/nf-core/bedtools/makewindows/tests/main.nf.test.snap
new file mode 100644
index 00000000000..22cfbc17253
--- /dev/null
+++ b/modules/nf-core/bedtools/makewindows/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "test-bedtools-makewindows-fai": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test2"
+                        },
+                        "test2.bed:md5,622d1f62786fe4239b76c53168f21c54"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test2"
+                        },
+                        "test2.bed:md5,622d1f62786fe4239b76c53168f21c54"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T14:03:31.430455"
+    },
+    "test-bedtools-makewindows-bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test2"
+                        },
+                        "test2.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test2"
+                        },
+                        "test2.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f797078cc8b8bac7e6906685d4867be5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T14:03:27.118372"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/makewindows/tests/nextflow.config b/modules/nf-core/bedtools/makewindows/tests/nextflow.config
new file mode 100644
index 00000000000..fa16733f166
--- /dev/null
+++ b/modules/nf-core/bedtools/makewindows/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: BEDTOOLS_MAKEWINDOWS {
+        ext.args = '-w 50 '
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 4aea9c2af1e..dbeafd70771 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -103,9 +103,6 @@ bedtools/intersect:
 bedtools/jaccard:
   - modules/nf-core/bedtools/jaccard/**
   - tests/modules/nf-core/bedtools/jaccard/**
-bedtools/makewindows:
-  - modules/nf-core/bedtools/makewindows/**
-  - tests/modules/nf-core/bedtools/makewindows/**
 bedtools/maskfasta:
   - modules/nf-core/bedtools/maskfasta/**
   - tests/modules/nf-core/bedtools/maskfasta/**
diff --git a/tests/modules/nf-core/bedtools/makewindows/main.nf b/tests/modules/nf-core/bedtools/makewindows/main.nf
deleted file mode 100644
index 13b59ea54e1..00000000000
--- a/tests/modules/nf-core/bedtools/makewindows/main.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BEDTOOLS_MAKEWINDOWS } from '../../../../../modules/nf-core/bedtools/makewindows/main.nf'
-
-workflow test_bedtools_makewindows_bed {
-
-    input = [
-        [ id:'test2'],
-        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    ]
-
-    BEDTOOLS_MAKEWINDOWS ( input )
-}
-
-workflow test_bedtools_makewindows_fai {
-
-    input = [
-        [ id:'test2'],
-        file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-    ]
-
-    BEDTOOLS_MAKEWINDOWS ( input )
-}
diff --git a/tests/modules/nf-core/bedtools/makewindows/nextflow.config b/tests/modules/nf-core/bedtools/makewindows/nextflow.config
deleted file mode 100644
index e8b8c3eae29..00000000000
--- a/tests/modules/nf-core/bedtools/makewindows/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: BEDTOOLS_MAKEWINDOWS {
-        ext.args = '-w 50 '
-    }
-
-}
diff --git a/tests/modules/nf-core/bedtools/makewindows/test.yml b/tests/modules/nf-core/bedtools/makewindows/test.yml
deleted file mode 100644
index f286c65abaa..00000000000
--- a/tests/modules/nf-core/bedtools/makewindows/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: bedtools makewindows test_bedtools_makewindows_bed
-  command: nextflow run ./tests/modules/nf-core/bedtools/makewindows -entry test_bedtools_makewindows_bed -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/makewindows/nextflow.config
-  tags:
-    - bedtools/makewindows
-    - bedtools
-  files:
-    - path: output/bedtools/test2.bed
-      md5sum: 0cf6ed2b6f470cd44a247da74ca4fe4e
-    - path: output/bedtools/versions.yml
-
-- name: bedtools makewindows test_bedtools_makewindows_fai
-  command: nextflow run ./tests/modules/nf-core/bedtools/makewindows -entry test_bedtools_makewindows_fai -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/makewindows/nextflow.config
-  tags:
-    - bedtools/makewindows
-    - bedtools
-  files:
-    - path: output/bedtools/test2.bed
-      md5sum: 622d1f62786fe4239b76c53168f21c54
-    - path: output/bedtools/versions.yml