diff --git a/modules/nf-core/blat/tests/main.nf.test b/modules/nf-core/blat/tests/main.nf.test
new file mode 100644
index 00000000000..8b07e5cf72f
--- /dev/null
+++ b/modules/nf-core/blat/tests/main.nf.test
@@ -0,0 +1,75 @@
+
+nextflow_process {
+
+    name "Test Process BLAT"
+    script "../main.nf"
+    process "BLAT"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "blat"
+    tag "seqtk/seq"
+
+    setup {
+        run("SEQTK_SEQ") {
+            script "../../seqtk/seq/main.nf"
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+    }
+
+    test("test-blat") {
+
+        when {
+            process {
+                """
+                input[0] = SEQTK_SEQ.out.fastx
+				input[1] = [
+				    [ id:'sarscov2' ],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-blat-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = SEQTK_SEQ.out.fastx
+				input[1] = [
+				    [ id:'sarscov2' ],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/blat/tests/main.nf.test.snap b/modules/nf-core/blat/tests/main.nf.test.snap
new file mode 100644
index 00000000000..d46a3320a6e
--- /dev/null
+++ b/modules/nf-core/blat/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "test-blat": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.psl:md5,6e2e5b3be48c84877f3c54b32bb9ec33"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a"
+                ],
+                "psl": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.psl:md5,6e2e5b3be48c84877f3c54b32bb9ec33"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T20:38:03.56409"
+    },
+    "test-blat-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.psl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a"
+                ],
+                "psl": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.psl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T20:38:09.736595"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/blat/tests/nextflow.config b/modules/nf-core/blat/tests/nextflow.config
new file mode 100644
index 00000000000..58bc3f25502
--- /dev/null
+++ b/modules/nf-core/blat/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: SEQTK_SEQ {
+        ext.args = '-A'
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index fda0a092c3f..e8273e4aa4c 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -52,9 +52,6 @@ bedtools/unionbedg:
 biohansel:
   - modules/nf-core/biohansel/**
   - tests/modules/nf-core/biohansel/**
-blat:
-  - modules/nf-core/blat/**
-  - tests/modules/nf-core/blat/**
 cadd:
   - modules/nf-core/cadd/**
   - tests/modules/nf-core/cadd/**
diff --git a/tests/modules/nf-core/blat/main.nf b/tests/modules/nf-core/blat/main.nf
deleted file mode 100644
index ad4184d084c..00000000000
--- a/tests/modules/nf-core/blat/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEQTK_SEQ } from '../../../../modules/nf-core/seqtk/seq/main.nf'
-include { BLAT      } from '../../../../modules/nf-core/blat/main.nf'
-
-workflow test_blat {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    sequences = [
-        [ id:'sarscov2' ],
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-    
-    SEQTK_SEQ ( input )
-    BLAT ( SEQTK_SEQ.out.fastx, sequences )
-}
diff --git a/tests/modules/nf-core/blat/nextflow.config b/tests/modules/nf-core/blat/nextflow.config
deleted file mode 100644
index f688ab59e76..00000000000
--- a/tests/modules/nf-core/blat/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-    withName: SEQTK_SEQ {
-        ext.args = '-A'
-    }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/blat/test.yml b/tests/modules/nf-core/blat/test.yml
deleted file mode 100644
index 0d8377d889e..00000000000
--- a/tests/modules/nf-core/blat/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: blat test_blat
-  command: nextflow run ./tests/modules/nf-core/blat -entry test_blat -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/blat/nextflow.config
-  tags:
-    - blat
-  files:
-    - path: output/blat/test.psl
-      md5sum: 6e2e5b3be48c84877f3c54b32bb9ec33
-    - path: output/blat/versions.yml