diff --git a/.github/conda_skip.yml b/.github/conda_skip.yml
index d14707c45f8..5865ef55a40 100644
--- a/.github/conda_skip.yml
+++ b/.github/conda_skip.yml
@@ -183,6 +183,8 @@ exclude:
   - profile: conda
     path: modules/nf-core/xeniumranger/import-segmentation
   - profile: conda
+    path: modules/nf-core/parabricks/mutectcaller
+ - profile: conda
     path: modules/nf-core/parabricks/dbsnp
   - profile: conda
     path: modules/nf-core/parabricks/indexgvcf
diff --git a/modules/nf-core/parabricks/mutectcaller/main.nf b/modules/nf-core/parabricks/mutectcaller/main.nf
index 4758cb14671..cb26790e95f 100644
--- a/modules/nf-core/parabricks/mutectcaller/main.nf
+++ b/modules/nf-core/parabricks/mutectcaller/main.nf
@@ -1,8 +1,10 @@
 process PARABRICKS_MUTECTCALLER {
     tag "$meta.id"
     label 'process_high'
+    label 'process_gpu'
+    stageInMode 'copy' // needed by the module to work properly - can be removed once fixed upstream
 
-    container "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1"
+    container "nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1"
 
     input:
     tuple val(meta), path(tumor_bam), path(tumor_bam_index),  path(normal_bam), path(normal_bam_index), path(interval_file)
@@ -30,6 +32,7 @@ process PARABRICKS_MUTECTCALLER {
     def interval_file_command = interval_file ? interval_file.collect{"--interval-file $it"}.join(' ') : ""
     def prepon_command = panel_of_normals ? "cp -L $panel_of_normals_index `readlink -f $panel_of_normals`.tbi && pbrun prepon --in-pon-file $panel_of_normals" : ""
     def postpon_command = panel_of_normals ? "pbrun postpon --in-vcf ${prefix}.vcf.gz --in-pon-file $panel_of_normals --out-vcf ${prefix}_annotated.vcf.gz" : ""
+    def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ""
     """
 
     # if panel of normals specified, run prepon
@@ -42,7 +45,7 @@ process PARABRICKS_MUTECTCALLER {
         --tumor-name ${meta.tumor_id} \\
         --out-vcf ${prefix}.vcf.gz \\
         $interval_file_command \\
-        --num-gpus $task.accelerator.request \\
+        $num_gpus \\
         $args
 
     # if panel of normals specified, run postpon
@@ -57,9 +60,9 @@ process PARABRICKS_MUTECTCALLER {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def postpon_command = panel_of_normals ? "touch ${prefix}_annotated.vcf.gz" : ""
+    def postpon_command = panel_of_normals ? "echo '' | gzip > ${prefix}_annotated.vcf.gz" : ""
     """
-    touch ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.stats
     $postpon_command
 
diff --git a/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test
new file mode 100644
index 00000000000..478b23a93a0
--- /dev/null
+++ b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test
@@ -0,0 +1,297 @@
+nextflow_process {
+
+    name "Test Process PARABRICKS_MUTECTCALLER"
+    script "../main.nf"
+    process "PARABRICKS_MUTECTCALLER"
+
+    tag "modules"
+    tag "parabricks/mutectcaller"
+    tag "modules_nfcore"
+    tag "parabricks"
+    tag "gpu"
+
+    test("human - bam") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                module_args = "--mutect-low-memory"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test',  tumor_id:'tumour' ],
+                    file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                    [], // index only neeeded if using intervals or tumor-normal calling
+                    [],
+                    [],
+                    []
+                ]
+                input[1] = [ // fasta
+                    [ id: 'reference' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    ]
+                input[2] = [] // pon
+                input[3] = [] // pon index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.vcf[0][1]).vcf.variantsMD5,
+                    process.out.stats,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    // test("human - bam - tn") {
+    // // tumor-normal calling not passing because of issue with readgroups in the test files
+    // // [PB Error][src/readers.cpp:1314] ID simulation01 maps to tm_simulation01, but PU is nm_simulation01 (different platform), exiting.
+
+    //     config "./nextflow.config"
+
+    //     when {
+    //         params {
+    //             module_args = "--in-normal-bam $normal_bam --normal-name $meta.normal_id --mutect-low-memory"
+    //         }
+    //         process {
+    //             """
+    //             input[0] = [
+    //                 [ id:'test',  tumor_id:'tumour', normal_id:'normal' ],
+    //                 file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+    //                 file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+    //                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+    //                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+    //                 []
+    //             ]
+    //             input[1] = [ // fasta
+    //                 [ id: 'reference' ], //genomics/homo_sapiens/genome/chr21/sequence/genome.fasta
+    //                 // file()
+    //                 file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    //                 ]
+    //             input[2] = [] // pon
+    //             input[3] = [] // pon index
+    //             """
+    //         }
+    //     }
+
+    //     then {
+    //         assertAll(
+    //             { assert process.success },
+    //             { assert snapshot(
+    //                 path(process.out.vcf[0][1]).vcf.variantsMD5,
+    //                 process.out.stats,
+    //                 process.out.versions
+    //                 ).match() }
+    //         )
+    //     }
+
+    // }
+
+    // test("human - bam - intervals") {
+
+    //     config "./nextflow.config"
+
+    //     when {
+    //         params {
+    //             module_args = "--mutect-low-memory"
+    //         }
+    //         process {
+    //             """
+    //             input[0] = [
+    //                 [ id:'test',  tumor_id:'tumor' ],
+    //                 file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+    //                 file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+    //                 [],
+    //                 [],
+    //                 file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    //             ]
+    //             input[1] = [ // fasta
+    //                 [ id: 'reference' ],
+    //                 file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    //                 ]
+    //             input[2] = [] // pon
+    //             input[3] = [] // pon index
+    //             """
+    //         }
+    //     }
+
+    //     then {
+    //         assertAll(
+    //             { assert process.success },
+    //             { assert snapshot(
+    //                 path(process.out.vcf[0][1]).vcf.variantsMD5,
+    //                 process.out.stats,
+    //                 process.out.versions
+    //                 ).match() }
+    //         )
+    //     }
+
+    // }
+
+    // test("human - bam - tn - intervals") {
+    // // tumor-normal calling not passing because of issue with readgroups in the test files
+    // // [PB Error][src/readers.cpp:1314] ID simulation01 maps to tm_simulation01, but PU is nm_simulation01 (different platform), exiting.
+
+    //     config "./nextflow.config"
+
+    //     when {
+    //         params {
+    //             module_args = "--in-normal-bam $normal_bam --normal-name $meta.normal_id --mutect-low-memory"
+    //         }
+    //         process {
+    //             """
+    //             input[0] = [
+    //                 [ id:'test',  tumor_id:'tumor', normal_id:'normal'],
+    //                 file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+    //                 file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+    //                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+    //                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+    //                 file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    //             ]
+    //             input[1] = [ // fasta
+    //                 [ id: 'reference' ],
+    //                 file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    //                 ]
+    //             input[2] = [] // pon
+    //             input[3] = [] // pon index
+    //             """
+    //         }
+    //     }
+
+    //     then {
+    //         assertAll(
+    //             { assert process.success },
+    //             { assert snapshot(
+    //                 path(process.out.vcf[0][1]).vcf.variantsMD5,
+    //                 process.out.stats,
+    //                 process.out.versions
+    //                 ).match() }
+    //         )
+    //     }
+
+    // }
+
+    // test("human - bam - pon") {
+    // // PON test not passing because the tool expects all chromosomes in the PON file to
+    // // be present in the reference genome.
+
+    //     config "./nextflow.config"
+
+    //     when {
+    //         params {
+    //             module_args = "--pon $panel_of_normals --mutect-low-memory"
+    //         }
+    //         process {
+    //             """
+    //             input[0] = [
+    //                 [ id:'test',  tumor_id:'tumour' ],
+    //                 file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+    //                 file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+    //                 [],
+    //                 [],
+    //                 file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    //             ]
+    //             input[1] = [ // fasta
+    //                 [ id: 'reference' ],
+    //                 file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    //                 ]
+    //             input[2] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
+    //             input[3] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
+    //             """
+    //         }
+    //     }
+
+    //     then {
+    //         assertAll(
+    //             { assert process.success },
+    //             { assert snapshot(
+    //                 path(process.out.vcf[0][1]).vcf.variantsMD5,
+    //                 process.out.stats,
+    //                 process.out.versions
+    //                 ).match() }
+    //         )
+    //     }
+
+    // }
+
+    test("human - bam - stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test',  tumor_id:'tumour' ],
+                    file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                    [], // index only neeeded if using intervals or tumor-normal calling
+                    [],
+                    [],
+                    []
+                ]
+                input[1] = [ // fasta
+                    [ id: 'reference' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    ]
+                input[2] = [] // pon
+                input[3] = [] // pon index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot( process.out ).match() }
+            )
+        }
+
+    }
+
+    test("human - bam - pon - stub") {
+
+        config "./nextflow.config"
+        options '-stub'
+
+        when {
+            params {
+                module_args = "--pon $panel_of_normals --mutect-low-memory"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test',  tumor_id:'tumour' ],
+                    file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                    [],
+                    [],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+                ]
+                input[1] = [ // fasta
+                    [ id: 'reference' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    ]
+                input[2] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
+                input[3] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot( process.out ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap
new file mode 100644
index 00000000000..960bdfae0ed
--- /dev/null
+++ b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap
@@ -0,0 +1,136 @@
+{
+    "human - bam - pon - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumour"
+                        },
+                        [
+                            "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_annotated.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,ce8c692a50f9b07c076f2e48a29d12bb"
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumour"
+                        },
+                        [
+                            "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_annotated.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ce8c692a50f9b07c076f2e48a29d12bb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-13T13:03:28.202892679"
+    },
+    "human - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,ce8c692a50f9b07c076f2e48a29d12bb"
+                ],
+                "stats": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "tumor_id": "tumour"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ce8c692a50f9b07c076f2e48a29d12bb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-13T12:37:04.215535795"
+    },
+    "human - bam": {
+        "content": [
+            "e9e77b557c40e868547a34dfca4fbd45",
+            [
+                [
+                    {
+                        "id": "test",
+                        "tumor_id": "tumour"
+                    },
+                    "test.vcf.gz.stats:md5,c58bc062c6f18d38df3892d15548d8c8"
+                ]
+            ],
+            [
+                "versions.yml:md5,ce8c692a50f9b07c076f2e48a29d12bb"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-13T13:02:31.029364594"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/parabricks/mutectcaller/tests/nextflow.config b/modules/nf-core/parabricks/mutectcaller/tests/nextflow.config
new file mode 100644
index 00000000000..1335bf3108f
--- /dev/null
+++ b/modules/nf-core/parabricks/mutectcaller/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: PARABRICKS_MUTECTCALLER {
+        ext.args = params.module_args
+    }
+
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 1147031e8b3..8678e2db900 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -398,9 +398,6 @@ parabricks/deepvariant:
 parabricks/haplotypecaller:
   - modules/nf-core/parabricks/haplotypecaller/**
   - tests/modules/nf-core/parabricks/haplotypecaller/**
-parabricks/mutectcaller:
-  - modules/nf-core/parabricks/mutectcaller/**
-  - tests/modules/nf-core/parabricks/mutectcaller/**
 paraclu:
   - modules/nf-core/paraclu/**
   - tests/modules/nf-core/paraclu/**
diff --git a/tests/modules/nf-core/parabricks/mutectcaller/main.nf b/tests/modules/nf-core/parabricks/mutectcaller/main.nf
deleted file mode 100644
index 2d4469a5456..00000000000
--- a/tests/modules/nf-core/parabricks/mutectcaller/main.nf
+++ /dev/null
@@ -1,113 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PARABRICKS_MUTECTCALLER } from '../../../../../modules/nf-core/parabricks/mutectcaller/main.nf'
-include { PARABRICKS_MUTECTCALLER as PARABRICKS_MUTECTCALLER_TN } from '../../../../../modules/nf-core/parabricks/mutectcaller/main.nf'
-include { PARABRICKS_MUTECTCALLER as PARABRICKS_MUTECTCALLER_TN_INTERVALS } from '../../../../../modules/nf-core/parabricks/mutectcaller/main.nf'
-include { PARABRICKS_MUTECTCALLER as PARABRICKS_MUTECTCALLER_PON } from '../../../../../modules/nf-core/parabricks/mutectcaller/main.nf'
-
-workflow test_parabricks_mutectcaller {
-    
-    input = [
-        [ id:'test',  tumor_id:'tumour' ],
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-        [], // index only neeeded if using intervals or tumor-normal calling
-        [],
-        [],
-        []
-    ]
-    fasta = [
-        [ id: 'homo_sapiens' ],
-        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-        ]
-    panel_of_normals = []
-    panel_of_normals_index = []
-
-    PARABRICKS_MUTECTCALLER ( input, fasta, panel_of_normals, panel_of_normals_index )
-}
-
-// tumor-normal calling not passing because of issue with readgroups in the test files
-// [PB Error][src/readers.cpp:1314] ID simulation01 maps to tm_simulation01, but PU is nm_simulation01 (different platform), exiting.
-workflow test_parabricks_mutectcaller_tn {
-    input = [
-        [ id:'test',  tumor_id:'tumour', normal_id:'normal' ],
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-        []      
-    ]
-    fasta = [
-         [ id: 'homo_sapiens' ],
-         file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-         ]
-    panel_of_normals = []
-    panel_of_normals_index = []
-
-    PARABRICKS_MUTECTCALLER_TN ( input, fasta, panel_of_normals, panel_of_normals_index )
-}
-
-workflow test_parabricks_mutectcaller_intervals {
-    input = [
-        [ id:'test',  tumor_id:'tumour' ],
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-        [],
-        [],
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)      
-    ]
-
-    fasta = [
-        [ id: 'homo_sapiens' ],
-        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-        ]
-
-    panel_of_normals = []
-    panel_of_normals_index = []
-
-    PARABRICKS_MUTECTCALLER ( input, fasta, panel_of_normals, panel_of_normals_index )
-}
-
-workflow test_parabricks_mutectcaller_tn_intervals {
-    input = [
-        [ id:'test',  tumor_id:'tumour', normal_id:'normal'],
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)      
-    ]
-    
-    fasta = [
-        [ id: 'homo_sapiens' ],
-        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-        ]
-    panel_of_normals = []
-    panel_of_normals_index = []
-
-    PARABRICKS_MUTECTCALLER_TN_INTERVALS ( input, fasta, panel_of_normals, panel_of_normals_index )
-}
-
-// PON test not passing because the tool expects all chromosomes in the PON file to 
-// be present in the reference genome. 
-workflow test_parabricks_mutectcaller_pon {
-    input = [
-        [ id:'test',  tumor_id:'tumour' ],
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-        [],
-        [],
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)      
-    ]
-
-    fasta = [
-           [ id: 'homo_sapiens' ],
-           file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-           ]
-
-    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
-    panel_of_normals_index = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
-
-    PARABRICKS_MUTECTCALLER_PON ( input, fasta, panel_of_normals, panel_of_normals_index )
-}
diff --git a/tests/modules/nf-core/parabricks/mutectcaller/nextflow.config b/tests/modules/nf-core/parabricks/mutectcaller/nextflow.config
deleted file mode 100644
index c3bfea0dc45..00000000000
--- a/tests/modules/nf-core/parabricks/mutectcaller/nextflow.config
+++ /dev/null
@@ -1,14 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: PARABRICKS_MUTECTCALLER_TN {
-        ext.args = { "--in-normal-bam $normal_bam --normal-name $meta.normal_id" }
-    }
-    withName: PARABRICKS_MUTECTCALLER_TN_INTERVALS {
-        ext.args = { "--in-normal-bam $normal_bam --normal-name $meta.normal_id" }
-    }
-    withName: PARABRICKS_MUTECTCALLER_PON {
-        ext.args = { "--pon $panel_of_normals" }
-    }
-}
diff --git a/tests/modules/nf-core/parabricks/mutectcaller/test.yml b/tests/modules/nf-core/parabricks/mutectcaller/test.yml
deleted file mode 100644
index 8674fc02c58..00000000000
--- a/tests/modules/nf-core/parabricks/mutectcaller/test.yml
+++ /dev/null
@@ -1,61 +0,0 @@
-- name: parabricks mutectcaller test_parabricks_mutectcaller
-  command: nextflow run ./tests/modules/nf-core/parabricks/mutectcaller -entry test_parabricks_mutectcaller -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/mutectcaller/nextflow.config -stub-run
-  tags:
-    - parabricks/mutectcaller
-    - parabricks
-  files:
-    - path: output/parabricks/test.vcf.gz
-      should_exist: true
-    - path: output/parabricks/test.vcf.gz.stats
-      should_exist: true
-    - path: output/parabricks/versions.yml
-
-- name: parabricks mutectcaller test_parabricks_mutectcaller_tn
-  command: nextflow run ./tests/modules/nf-core/parabricks/mutectcaller -entry test_parabricks_mutectcaller_tn -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/mutectcaller/nextflow.config -stub-run
-  tags:
-    - parabricks/mutectcaller
-    - parabricks
-  files:
-    - path: output/parabricks/test.vcf.gz
-      should_exist: true
-    - path: output/parabricks/test.vcf.gz.stats
-      should_exist: true
-    - path: output/parabricks/versions.yml
-
-- name: parabricks mutectcaller test_parabricks_mutectcaller_intervals
-  command: nextflow run ./tests/modules/nf-core/parabricks/mutectcaller -entry test_parabricks_mutectcaller_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/mutectcaller/nextflow.config -stub-run
-  tags:
-    - parabricks/mutectcaller
-    - parabricks
-  files:
-    - path: output/parabricks/test.vcf.gz
-      should_exist: true
-    - path: output/parabricks/test.vcf.gz.stats
-      should_exist: true
-    - path: output/parabricks/versions.yml
-
-- name: parabricks mutectcaller test_parabricks_mutectcaller_tn_intervals
-  command: nextflow run ./tests/modules/nf-core/parabricks/mutectcaller -entry test_parabricks_mutectcaller_tn_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/mutectcaller/nextflow.config -stub-run
-  tags:
-    - parabricks/mutectcaller
-    - parabricks
-  files:
-    - path: output/parabricks/test.vcf.gz
-      should_exist: true
-    - path: output/parabricks/test.vcf.gz.stats
-      should_exist: true
-    - path: output/parabricks/versions.yml
-
-- name: parabricks mutectcaller test_parabricks_mutectcaller_pon
-  command: nextflow run ./tests/modules/nf-core/parabricks/mutectcaller -entry test_parabricks_mutectcaller_pon -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/mutectcaller/nextflow.config -stub-run
-  tags:
-    - parabricks/mutectcaller
-    - parabricks
-  files:
-    - path: output/parabricks/test.vcf.gz
-      should_exist: true
-    - path: output/parabricks/test_annotated.vcf.gz
-      should_exist: true
-    - path: output/parabricks/test.vcf.gz.stats
-      should_exist: true
-    - path: output/parabricks/versions.yml
diff --git a/tests/modules/nf-core/parabricks/mutectcaller/test_GPU_config.txt b/tests/modules/nf-core/parabricks/mutectcaller/test_GPU_config.txt
deleted file mode 100644
index 32b2011adef..00000000000
--- a/tests/modules/nf-core/parabricks/mutectcaller/test_GPU_config.txt
+++ /dev/null
@@ -1,18 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    memory = "15.GB"
-    cpus  = 4
-    accelerator = 1
-    withName: PARABRICKS_MUTECTCALLER_TN {
-        ext.args = { "--in-normal-bam $normal_bam --normal-name $meta.normal_id" }
-    }
-    withName: PARABRICKS_MUTECTCALLER_TN_INTERVALS {
-        ext.args = { "--in-normal-bam $normal_bam --normal-name $meta.normal_id" }
-    }
-    withName: PARABRICKS_MUTECTCALLER_PON {
-        ext.args = { "--pon $panel_of_normals" }
-    }
-}
-docker.runOptions = "--gpus all"
-singularity.runOptions = "--nv"
\ No newline at end of file
diff --git a/tests/modules/nf-core/parabricks/mutectcaller/test_GPU_yml.txt b/tests/modules/nf-core/parabricks/mutectcaller/test_GPU_yml.txt
deleted file mode 100644
index d06202c8aaa..00000000000
--- a/tests/modules/nf-core/parabricks/mutectcaller/test_GPU_yml.txt
+++ /dev/null
@@ -1,62 +0,0 @@
-- name: parabricks mutectcaller test_parabricks_mutectcaller
-  command: nextflow run ./tests/modules/nf-core/parabricks/mutectcaller -entry test_parabricks_mutectcaller -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/mutectcaller/nextflow.config
-  tags:
-    - parabricks/mutectcaller
-    - parabricks
-  files:
-    - path: output/parabricks/test.vcf.gz
-      md5sum: 8c674cd93a83b9e66794db83c9b29926
-    - path: output/parabricks/test.vcf.gz.stats
-      md5sum: c58bc062c6f18d38df3892d15548d8c8
-    - path: output/parabricks/versions.yml
-
-- name: parabricks mutectcaller test_parabricks_mutectcaller_tn
-  command: nextflow run ./tests/modules/nf-core/parabricks/mutectcaller -entry test_parabricks_mutectcaller_tn -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/mutectcaller/nextflow.config
-  tags:
-    - parabricks/mutectcaller
-    - parabricks
-  files:
-    - path: output/parabricks/test.vcf.gz
-      should_exist: true
-    - path: output/parabricks/test.vcf.gz.stats
-      should_exist: true
-    - path: output/parabricks/versions.yml
-    
-- name: parabricks mutectcaller test_parabricks_mutectcaller_intervals
-  command: nextflow run ./tests/modules/nf-core/parabricks/mutectcaller -entry test_parabricks_mutectcaller_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/mutectcaller/nextflow.config
-  tags:
-    - parabricks/mutectcaller
-    - parabricks
-  files:
-    - path: output/parabricks/test.vcf.gz
-      md5sum: 37fb3c2e9c96df940b5201f66962c79f
-    - path: output/parabricks/test.vcf.gz.stats
-      md5sum: 730b6c6fd6c35aa7752c2455e9e50847
-    - path: output/parabricks/versions.yml
-
-- name: parabricks mutectcaller test_parabricks_mutectcaller_tn_intervals
-  command: nextflow run ./tests/modules/nf-core/parabricks/mutectcaller -entry test_parabricks_mutectcaller_tn_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/mutectcaller/nextflow.config
-  tags:
-    - parabricks/mutectcaller
-    - parabricks
-  files:
-    - path: output/parabricks/test.vcf.gz
-      should_exist: true
-    - path: output/parabricks/test.vcf.gz.stats
-      should_exist: true
-    - path: output/parabricks/versions.yml
-    
-- name: parabricks mutectcaller test_parabricks_mutectcaller_pon
-  command: nextflow run ./tests/modules/nf-core/parabricks/mutectcaller -entry test_parabricks_mutectcaller_pon -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/mutectcaller/nextflow.config
-  tags:
-    - parabricks/mutectcaller
-    - parabricks
-  files:
-    - path: output/parabricks/test.vcf.gz
-      should_exist: true
-    - path: output/parabricks/test_annotated.vcf.gz
-      should_exist: true
-    - path: output/parabricks/test.vcf.gz.stats
-      should_exist: true
-    - path: output/parabricks/versions.yml
-    
\ No newline at end of file