diff --git a/modules/nf-core/pairtools/dedup/tests/main.nf.test b/modules/nf-core/pairtools/dedup/tests/main.nf.test
new file mode 100644
index 00000000000..41bbfabb45c
--- /dev/null
+++ b/modules/nf-core/pairtools/dedup/tests/main.nf.test
@@ -0,0 +1,39 @@
+
+nextflow_process {
+
+    name "Test Process PAIRTOOLS_DEDUP"
+    script "../main.nf"
+    process "PAIRTOOLS_DEDUP"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pairtools"
+    tag "pairtools/dedup"
+
+    test("test-pairtools-dedup") {
+        
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.4dedup.pairsam', checkIfExists: true) ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.pairs[0][1]).linesGzip[3..7],
+					process.out.stat,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+    
+}
diff --git a/modules/nf-core/pairtools/dedup/tests/main.nf.test.snap b/modules/nf-core/pairtools/dedup/tests/main.nf.test.snap
new file mode 100644
index 00000000000..46dcf9654b7
--- /dev/null
+++ b/modules/nf-core/pairtools/dedup/tests/main.nf.test.snap
@@ -0,0 +1,30 @@
+{
+    "test-pairtools-dedup": {
+        "content": [
+            [
+                "#genome_assembly: unknown",
+                "#chromosomes: chr1 chr2",
+                "#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2",
+                "readid3\tchr1\t1\tchr1\t20\t+\t+\tUU\t.\t.",
+                "readid5\tchr1\t1\tchr1\t25\t+\t+\tUU\t.\t."
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.dedup.pairs.stat:md5,94682d1bc608ade150dd11993fbfd2a3"
+                ]
+            ],
+            [
+                "versions.yml:md5,485fbdd68f35d563c8559e1afedc4c53"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T11:23:16.451408"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/pairtools/dedup/tests/nextflow.config b/modules/nf-core/pairtools/dedup/tests/nextflow.config
new file mode 100644
index 00000000000..d0cfe51f1a2
--- /dev/null
+++ b/modules/nf-core/pairtools/dedup/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: PAIRTOOLS_DEDUP {
+        ext.prefix = { "${meta.id}.dedup" }
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index b698856bbae..e68c1f9d130 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1001,9 +1001,6 @@ paftools/sam2paf:
 pairix:
   - modules/nf-core/pairix/**
   - tests/modules/nf-core/pairix/**
-pairtools/dedup:
-  - modules/nf-core/pairtools/dedup/**
-  - tests/modules/nf-core/pairtools/dedup/**
 pairtools/flip:
   - modules/nf-core/pairtools/flip/**
   - tests/modules/nf-core/pairtools/flip/**
diff --git a/tests/modules/nf-core/pairtools/dedup/main.nf b/tests/modules/nf-core/pairtools/dedup/main.nf
deleted file mode 100644
index 408dd02da09..00000000000
--- a/tests/modules/nf-core/pairtools/dedup/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PAIRTOOLS_DEDUP } from '../../../../../modules/nf-core/pairtools/dedup/main.nf'
-
-workflow test_pairtools_dedup {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['generic']['pairtools']['mock_4dedup_pairsam'], checkIfExists: true) ]
-
-    PAIRTOOLS_DEDUP ( input )
-}
diff --git a/tests/modules/nf-core/pairtools/dedup/nextflow.config b/tests/modules/nf-core/pairtools/dedup/nextflow.config
deleted file mode 100644
index b47fab16594..00000000000
--- a/tests/modules/nf-core/pairtools/dedup/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: PAIRTOOLS_DEDUP {
-        ext.prefix = { "${meta.id}.dedup" }
-    }
-
-}
diff --git a/tests/modules/nf-core/pairtools/dedup/test.yml b/tests/modules/nf-core/pairtools/dedup/test.yml
deleted file mode 100644
index 722ec9f66d9..00000000000
--- a/tests/modules/nf-core/pairtools/dedup/test.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-- name: pairtools dedup test_pairtools_dedup
-  command: nextflow run ./tests/modules/nf-core/pairtools/dedup -entry test_pairtools_dedup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pairtools/dedup/nextflow.config
-  tags:
-    - pairtools/dedup
-    - pairtools
-  files:
-    - path: output/pairtools/test.dedup.pairs.gz
-      md5sum: 7ed7436793eccc77aeacb25fbe7816aa
-    - path: output/pairtools/test.dedup.pairs.stat
-      md5sum: 94682d1bc608ade150dd11993fbfd2a3