diff --git a/modules/nf-core/hypo/meta.yml b/modules/nf-core/hypo/meta.yml
index 36a7e714f752..002b418f5c8c 100644
--- a/modules/nf-core/hypo/meta.yml
+++ b/modules/nf-core/hypo/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/kensung-lab/hypo/blob/master/README.md"
       tool_dev_url: "https://github.com/kensung-lab/hypo"
       doi: "10.1101/2019.12.19.882506"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/hypo/tests/main.nf.test b/modules/nf-core/hypo/tests/main.nf.test
new file mode 100644
index 000000000000..06fb15906f07
--- /dev/null
+++ b/modules/nf-core/hypo/tests/main.nf.test
@@ -0,0 +1,76 @@
+
+nextflow_process {
+
+    name "Test Process HYPO"
+    script "../main.nf"
+    process "HYPO"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hypo"
+
+    test("test-hypo") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+				]
+				input[1] = [
+				    [ id:'test', single_end:false ], // meta map
+				    [
+				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+				    ]
+				]
+				input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[3] = 29903
+				input[4] = 5
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-hypo-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+				]
+				input[1] = [
+				    [ id:'test', single_end:false ], // meta map
+				    [
+				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+				    ]
+				]
+				input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[3] = 29903
+				input[4] = 5
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/hypo/tests/main.nf.test.snap b/modules/nf-core/hypo/tests/main.nf.test.snap
new file mode 100644
index 000000000000..999ec08c13df
--- /dev/null
+++ b/modules/nf-core/hypo/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "test-hypo-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:15:49.822312"
+    },
+    "test-hypo": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d326ff4fc91e25617c43d678f68187ad"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d326ff4fc91e25617c43d678f68187ad"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:15:37.149543"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 9da0e502f277..acdb090f30e2 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -362,9 +362,6 @@ hmtnote/annotate:
 homer/makeucscfile:
   - modules/nf-core/homer/makeucscfile/**
   - tests/modules/nf-core/homer/makeucscfile/**
-hypo:
-  - modules/nf-core/hypo/**
-  - tests/modules/nf-core/hypo/**
 icountmini/metagene:
   - modules/nf-core/icountmini/metagene/**
   - tests/modules/nf-core/icountmini/metagene/**
diff --git a/tests/modules/nf-core/hypo/main.nf b/tests/modules/nf-core/hypo/main.nf
deleted file mode 100644
index 89b169fc58eb..000000000000
--- a/tests/modules/nf-core/hypo/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HYPO } from '../../../../modules/nf-core/hypo/main.nf'
-
-workflow test_hypo {
-    
-    bam_sr = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
-    reads = [
-        [ id:'test', single_end:false ], // meta map
-        [
-            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-    draft = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    genome_size = 29903
-    reads_coverage = 5
-    HYPO ( bam_sr, reads, draft, genome_size, reads_coverage )
-}
diff --git a/tests/modules/nf-core/hypo/nextflow.config b/tests/modules/nf-core/hypo/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/hypo/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/hypo/test.yml b/tests/modules/nf-core/hypo/test.yml
deleted file mode 100644
index f298d04ea897..000000000000
--- a/tests/modules/nf-core/hypo/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: "hypo"
-  command: nextflow run ./tests/modules/nf-core/hypo -entry test_hypo -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hypo/nextflow.config
-  tags:
-    - "hypo"
-  files:
-    - path: "output/hypo/test.fasta"
-      md5sum: d326ff4fc91e25617c43d678f68187ad
-    - path: "output/hypo/versions.yml"
-      md5sum: 34233e4c5530683bf3c9e890e2b20e91