diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf
index 6329391c837..a2c7666b520 100644
--- a/modules/nf-core/vardictjava/main.nf
+++ b/modules/nf-core/vardictjava/main.nf
@@ -14,7 +14,7 @@ process VARDICTJAVA {
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
-    path "versions.yml"           , emit: versions
+    path "versions.yml"              , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,9 +25,12 @@ process VARDICTJAVA {
     def args3 = task.ext.args3 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
+    // Don't run test scripts when -fisher has been used by vardictjava
+    def run_test = !args.contains("-fisher")
+
     def somatic = bams instanceof List && bams.size() == 2 ? true : false
     def input = somatic ? "-b \"${bams[0]}|${bams[1]}\"" : "-b ${bams}"
-    def filter = somatic ? "testsomatic.R" : "teststrandbias.R"
+    def test = run_test ? somatic ? "| testsomatic.R" : "| teststrandbias.R" : ""
     def convert_to_vcf = somatic ? "var2vcf_paired.pl" : "var2vcf_valid.pl"
     """
     export JAVA_OPTS='"-Xms${task.memory.toMega()/4}m" "-Xmx${task.memory.toGiga()}g" "-Dsamjdk.reference_fasta=${fasta}"'
@@ -37,7 +40,7 @@ process VARDICTJAVA {
         -th ${task.cpus} \\
         -G ${fasta} \\
         ${bed} \\
-    | ${filter} \\
+    ${test} \\
     | ${convert_to_vcf} \\
         ${args2} \\
     | bgzip ${args3} --threads ${task.cpus} > ${prefix}.vcf.gz
@@ -50,9 +53,6 @@ process VARDICTJAVA {
     """
 
     stub:
-    def args = task.ext.args ?: '-c 1 -S 2 -E 3'
-    def args2 = task.ext.args2 ?: ''
-    def args3 = task.ext.args3 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
diff --git a/modules/nf-core/vardictjava/tests/main.nf.test b/modules/nf-core/vardictjava/tests/main.nf.test
index 8e5fec10266..31e1058cad8 100644
--- a/modules/nf-core/vardictjava/tests/main.nf.test
+++ b/modules/nf-core/vardictjava/tests/main.nf.test
@@ -10,9 +10,6 @@ nextflow_process {
     test("homo_sapiens - [bam, bai, bed] - fasta - fai") {
 
         when {
-            params {
-                outdir = $outputDir
-            }
             process {
                 """
                 input[0] = Channel.value([
@@ -47,9 +44,6 @@ nextflow_process {
     test("homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai") {
 
         when {
-            params {
-                outdir = $outputDir
-            }
             process {
                 """
                 input[0] = Channel.value([
@@ -87,4 +81,75 @@ nextflow_process {
 
     }
 
+    test("homo_sapiens - [bam, bai, bed] - fasta - fai - fisher") {
+
+        config "./nextflow.config"
+        when {
+            process {
+                """
+                input[0] = Channel.value([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                ])
+                input[1] = [
+                    [id:"ref"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [id:"ref"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+            
+            
+        }
+
+    }
+
+    test("homo_sapiens - [bam, bai, bed] - fasta - fai - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.value([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                ])
+                input[1] = [
+                    [id:"ref"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [id:"ref"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+            
+            
+        }
+
+    }
+
 }
diff --git a/modules/nf-core/vardictjava/tests/main.nf.test.snap b/modules/nf-core/vardictjava/tests/main.nf.test.snap
index c32a68b7424..35674ed1782 100644
--- a/modules/nf-core/vardictjava/tests/main.nf.test.snap
+++ b/modules/nf-core/vardictjava/tests/main.nf.test.snap
@@ -27,10 +27,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-04T19:08:38.328190023"
+        "timestamp": "2024-10-07T16:05:15.117453312"
     },
     "homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai": {
         "content": [
@@ -60,9 +60,75 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-04T19:08:54.416661915"
+        "timestamp": "2024-10-07T16:05:26.932438089"
+    },
+    "homo_sapiens - [bam, bai, bed] - fasta - fai - fisher": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-07T16:05:38.456816851"
+    },
+    "homo_sapiens - [bam, bai, bed] - fasta - fai - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-07T16:05:48.440804849"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/vardictjava/tests/nextflow.config b/modules/nf-core/vardictjava/tests/nextflow.config
new file mode 100644
index 00000000000..c6e8571bd41
--- /dev/null
+++ b/modules/nf-core/vardictjava/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = "-c 1 -S 2 -E 3 -fisher"
+}
\ No newline at end of file