diff --git a/modules/nf-core/pairtools/sort/tests/main.nf.test b/modules/nf-core/pairtools/sort/tests/main.nf.test
new file mode 100644
index 00000000000..a4e789bc58d
--- /dev/null
+++ b/modules/nf-core/pairtools/sort/tests/main.nf.test
@@ -0,0 +1,38 @@
+
+nextflow_process {
+
+    name "Test Process PAIRTOOLS_SORT"
+    script "../main.nf"
+    process "PAIRTOOLS_SORT"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pairtools"
+    tag "pairtools/sort"
+
+    test("test-pairtools-sort") {
+        
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pairtools/mock.pairsam', checkIfExists: true) ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.sorted[0][1]).linesGzip[3..7],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+    
+}
diff --git a/modules/nf-core/pairtools/sort/tests/main.nf.test.snap b/modules/nf-core/pairtools/sort/tests/main.nf.test.snap
new file mode 100644
index 00000000000..1b22f32856f
--- /dev/null
+++ b/modules/nf-core/pairtools/sort/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "test-pairtools-sort": {
+        "content": [
+            [
+                "#genome_assembly: unknown",
+                "#chromosomes: : chr1 chr2 chr3",
+                "#chromsize: chr2 100",
+                "#chromsize: chr3 100",
+                "#chromsize: chr1 100"
+            ],
+            [
+                "versions.yml:md5,6f5e6b4260ee11d35e306d2e085fb762"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T11:12:01.451816"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/pairtools/sort/tests/nextflow.config b/modules/nf-core/pairtools/sort/tests/nextflow.config
new file mode 100644
index 00000000000..566f8da2d56
--- /dev/null
+++ b/modules/nf-core/pairtools/sort/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: PAIRTOOLS_SORT {
+        ext.prefix = { "${meta.id}.sorted" }
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index b698856bbae..aae32b989eb 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1019,9 +1019,6 @@ pairtools/restrict:
 pairtools/select:
   - modules/nf-core/pairtools/select/**
   - tests/modules/nf-core/pairtools/select/**
-pairtools/sort:
-  - modules/nf-core/pairtools/sort/**
-  - tests/modules/nf-core/pairtools/sort/**
 pairtools/stats:
   - modules/nf-core/pairtools/stats/**
   - tests/modules/nf-core/pairtools/stats/**
diff --git a/tests/modules/nf-core/pairtools/sort/main.nf b/tests/modules/nf-core/pairtools/sort/main.nf
deleted file mode 100644
index 82f61cf7f4d..00000000000
--- a/tests/modules/nf-core/pairtools/sort/main.nf
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PAIRTOOLS_SORT } from '../../../../../modules/nf-core/pairtools/sort/main.nf'
-
-workflow test_pairtools_sort {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['generic']['pairtools']['mock_pairsam'], checkIfExists: true) ]
-
-    PAIRTOOLS_SORT ( input )
-}
diff --git a/tests/modules/nf-core/pairtools/sort/nextflow.config b/tests/modules/nf-core/pairtools/sort/nextflow.config
deleted file mode 100644
index dfaf60532ce..00000000000
--- a/tests/modules/nf-core/pairtools/sort/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: PAIRTOOLS_SORT {
-        ext.prefix = { "${meta.id}.sorted" }
-    }
-
-}
diff --git a/tests/modules/nf-core/pairtools/sort/test.yml b/tests/modules/nf-core/pairtools/sort/test.yml
deleted file mode 100644
index 4d5f2d81003..00000000000
--- a/tests/modules/nf-core/pairtools/sort/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: pairtools sort test_pairtools_sort
-  command: nextflow run ./tests/modules/nf-core/pairtools/sort -entry test_pairtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pairtools/sort/nextflow.config
-  tags:
-    - pairtools/sort
-    - pairtools
-  files:
-    - path: output/pairtools/test.sorted.pairs.gz # Not using MD5 checksum because the file includes the run paths, which are different under Conda
-      contains:
-        - "readid08\t!\t0\t!\t0\t-\t-\tWW\treadid08"