diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test
new file mode 100644
index 00000000000..2e3688a779d
--- /dev/null
+++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test
@@ -0,0 +1,64 @@
+
+nextflow_process {
+
+    name "Test Process GATK4_FASTQTOSAM"
+    script "../main.nf"
+    process "GATK4_FASTQTOSAM"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/fastqtosam"
+
+    test("test-gatk4-fastqtosam-single-end") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-gatk4-fastqtosam-paired-end") {
+
+        when {
+            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),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap
new file mode 100644
index 00000000000..554480a24b7
--- /dev/null
+++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap
@@ -0,0 +1,28 @@
+{
+    "test-gatk4-fastqtosam-single-end": {
+        "content": [
+            "e6a4aa204d980e177a0458596f0a70ac",
+            [
+                "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:29:12.362942"
+    },
+    "test-gatk4-fastqtosam-paired-end": {
+        "content": [
+            "e6a4aa204d980e177a0458596f0a70ac",
+            [
+                "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T12:29:22.385798"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 4aea9c2af1e..8993f36704b 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -464,9 +464,6 @@ gatk4/createsomaticpanelofnormals:
 gatk4/determinegermlinecontigploidy:
   - modules/nf-core/gatk4/determinegermlinecontigploidy/**
   - tests/modules/nf-core/gatk4/determinegermlinecontigploidy/**
-gatk4/fastqtosam:
-  - modules/nf-core/gatk4/fastqtosam/**
-  - tests/modules/nf-core/gatk4/fastqtosam/**
 gatk4/filterintervals:
   - modules/nf-core/gatk4/filterintervals/**
   - tests/modules/nf-core/gatk4/filterintervals/**
diff --git a/tests/modules/nf-core/gatk4/fastqtosam/main.nf b/tests/modules/nf-core/gatk4/fastqtosam/main.nf
deleted file mode 100644
index 0a3aef644d4..00000000000
--- a/tests/modules/nf-core/gatk4/fastqtosam/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_FASTQTOSAM } from '../../../../../modules/nf-core/gatk4/fastqtosam/main.nf'
-
-workflow test_gatk4_fastqtosam_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-            ]
-
-    GATK4_FASTQTOSAM ( input )
-}
-
-workflow test_gatk4_fastqtosam_paired_end {
-    input = [ [ 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)
-            ]
-
-    GATK4_FASTQTOSAM ( input )
-}
diff --git a/tests/modules/nf-core/gatk4/fastqtosam/nextflow.config b/tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/gatk4/fastqtosam/test.yml b/tests/modules/nf-core/gatk4/fastqtosam/test.yml
deleted file mode 100644
index 482284d5956..00000000000
--- a/tests/modules/nf-core/gatk4/fastqtosam/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end
-  command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/fastqtosam
-  files:
-    - path: output/gatk4/test.bam
-
-- name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
-  command: nextflow run ./tests/modules/nf-core/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/gatk4/fastqtosam/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/fastqtosam
-  files:
-    - path: output/gatk4/test.bam
-    - path: output/gatk4/versions.yml