diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf
index 3a9fbb4e07a..f180f74975c 100644
--- a/modules/nf-core/gatk4/genotypegvcfs/main.nf
+++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf
@@ -8,12 +8,12 @@ process GATK4_GENOTYPEGVCFS {
         'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index)
-    path  fasta
-    path  fai
-    path  dict
-    path  dbsnp
-    path  dbsnp_tbi
+    tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(dict)
+    tuple val(meta5), path(dbsnp)
+    tuple val(meta6), path(dbsnp_tbi)
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
@@ -26,7 +26,7 @@ process GATK4_GENOTYPEGVCFS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def gvcf_command = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf"
+    def input_command = input.name.endsWith(".vcf") || input.name.endsWith(".vcf.gz") ? "$input" : "gendb://$input"
     def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : ""
     def interval_command = intervals ? "--intervals $intervals" : ""
 
@@ -39,7 +39,7 @@ process GATK4_GENOTYPEGVCFS {
     """
     gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\
         GenotypeGVCFs \\
-        --variant $gvcf_command \\
+        --variant $input_command \\
         --output ${prefix}.vcf.gz \\
         --reference $fasta \\
         $interval_command \\
@@ -57,7 +57,7 @@ process GATK4_GENOTYPEGVCFS {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    touch ${prefix}.vcf.gz
+    echo | gzip > ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/gatk4/genotypegvcfs/meta.yml b/modules/nf-core/gatk4/genotypegvcfs/meta.yml
index 8f1e377eb91..eb704364b48 100644
--- a/modules/nf-core/gatk4/genotypegvcfs/meta.yml
+++ b/modules/nf-core/gatk4/genotypegvcfs/meta.yml
@@ -20,10 +20,10 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - gvcf:
+  - input:
       type: file
       description: |
-        gVCF(.gz) file or to a GenomicsDB
+        gVCF(.gz) file or a GenomicsDB
       pattern: "*.{vcf,vcf.gz}"
   - gvcf_index:
       type: file
@@ -36,22 +36,47 @@ input:
   - intervals_index:
       type: file
       description: Interval index file (optional)
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing fasta information
+        e.g. [ id:'test' ]
   - fasta:
       type: file
       description: Reference fasta file
       pattern: "*.fasta"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing fai information
+        e.g. [ id:'test' ]
   - fai:
       type: file
       description: Reference fasta index file
       pattern: "*.fai"
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing dict information
+        e.g. [ id:'test' ]
   - dict:
       type: file
       description: Reference fasta sequence dict file
       pattern: "*.dict"
+  - meta5:
+      type: map
+      description: |
+        Groovy Map containing dbsnp information
+        e.g. [ id:'test' ]
   - dbsnp:
       type: file
       description: dbSNP VCF file
       pattern: "*.vcf.gz"
+  - meta6:
+      type: map
+      description: |
+        Groovy Map containing dbsnp tbi information
+        e.g. [ id:'test' ]
   - dbsnp_tbi:
       type: file
       description: dbSNP VCF index file
diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test
new file mode 100644
index 00000000000..25bc2d3806b
--- /dev/null
+++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test
@@ -0,0 +1,285 @@
+nextflow_process {
+
+    name "Test Process GATK4_GENOTYPEGVCFS"
+    script "../main.nf"
+    process "GATK4_GENOTYPEGVCFS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/genotypegvcfs"
+    tag "untar"
+
+    setup {
+        run("UNTAR") {
+            script "../../../untar/main.nf"
+            process {
+                """
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] },
+                    process.out.tbi.collect { [it[0], file(it[1]).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [
+                    [id:"dbsnp"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists:true)
+                ]
+                input[5] = [
+                    [id:"dbsnp"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists:true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] },
+                    process.out.tbi.collect { [it[0], file(it[1]).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true),
+                    []
+                ]
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] },
+                    process.out.tbi.collect { [it[0], file(it[1]).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [gendb, [], [], []], fasta, fai, dict, [], []") {
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta, gendb -> [ meta, gendb, [], [], []] }
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] },
+                    process.out.tbi.collect { [it[0], file(it[1]).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []") {
+
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta, gendb -> 
+                    [ 
+                        meta,
+                        gendb,
+                        [],
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true),
+                        []
+                    ] 
+                }
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] },
+                    process.out.tbi.collect { [it[0], file(it[1]).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:"test"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true),
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [id:"fasta"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
+                ]
+                input[2] = [
+                    [id:"fai"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
+                ]
+                input[3] = [
+                    [id:"dict"],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true)
+                ]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap
new file mode 100644
index 00000000000..1621618e7a9
--- /dev/null
+++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap
@@ -0,0 +1,191 @@
+{
+    "homo_sapiens - [gendb, [], [], []], fasta, fai, dict, [], []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "1ab95fbc5ec55b208f3001572bec54fa"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi"
+                ]
+            ],
+            [
+                "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-04T14:27:24.926097884"
+    },
+    "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "1ab95fbc5ec55b208f3001572bec54fa"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi"
+                ]
+            ],
+            [
+                "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-04T14:26:24.426228557"
+    },
+    "homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "1ab95fbc5ec55b208f3001572bec54fa"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi"
+                ]
+            ],
+            [
+                "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-04T14:27:04.179308513"
+    },
+    "homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "9b7d476515e07e5486633c42abd86cc"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi"
+                ]
+            ],
+            [
+                "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-04T14:26:43.9088684"
+    },
+    "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3"
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-04T14:19:57.615552867"
+    },
+    "homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "1ab95fbc5ec55b208f3001572bec54fa"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi"
+                ]
+            ],
+            [
+                "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-04T14:27:46.189794941"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index defa2252fed..27e6d8ed9ca 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -233,9 +233,6 @@ gatk4/determinegermlinecontigploidy:
 gatk4/filtervarianttranches:
   - modules/nf-core/gatk4/filtervarianttranches/**
   - tests/modules/nf-core/gatk4/filtervarianttranches/**
-gatk4/genotypegvcfs:
-  - modules/nf-core/gatk4/genotypegvcfs/**
-  - tests/modules/nf-core/gatk4/genotypegvcfs/**
 gatk4/germlinecnvcaller:
   - modules/nf-core/gatk4/germlinecnvcaller/**
   - tests/modules/nf-core/gatk4/germlinecnvcaller/**
diff --git a/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf b/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf
deleted file mode 100644
index 06423b29d1d..00000000000
--- a/tests/modules/nf-core/gatk4/genotypegvcfs/main.nf
+++ /dev/null
@@ -1,182 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GATK4_GENOTYPEGVCFS } from '../../../../../modules/nf-core/gatk4/genotypegvcfs/main.nf'
-include { UNTAR               } from '../../../../../modules/nf-core/untar/main.nf'
-
-// Basic parameters with uncompressed VCF input
-workflow test_gatk4_genotypegvcfs_vcf_input {
-
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true),
-            [],
-            []
-        ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
-}
-
-// Basic parameters with compressed VCF input
-workflow test_gatk4_genotypegvcfs_gz_input {
-
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
-            [],
-            []
-        ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
-}
-
-// Basic parameters + optional dbSNP
-workflow test_gatk4_genotypegvcfs_gz_input_dbsnp {
-
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
-            [],
-            []
-        ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi)
-}
-
-// Basic parameters + optional intervals
-workflow test_gatk4_genotypegvcfs_gz_input_intervals {
-
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ,
-            []
-            ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
-}
-
-// Basic parameters + optional dbSNP + optional intervals
-workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
-
-    input = [ [ id:'test' ], // meta map
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
-            file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
-            []
-        ]
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )
-}
-
-// Basic parameters with GenomicsDB input
-workflow test_gatk4_genotypegvcfs_gendb_input {
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.map{ it[1] }.collect()
-    gendb.add([])
-    gendb.add([])
-    gendb.add([])
-
-    input = Channel.of([ id:'test' ]).combine(gendb)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [])
-}
-
-// Basic parameters with GenomicsDB + optional dbSNP
-workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.map{ it[1] }.collect()
-    gendb.add([])
-    gendb.add([])
-    gendb.add([])
-    input = Channel.of([ id:'test' ]).combine(gendb)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi)
-}
-
-// Basic parameters with GenomicsDB + optional intervals
-workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.map{ it[1] }.collect()
-    gendb.add([])
-    gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
-    gendb.add([])
-
-    input = Channel.of([ id:'test' ]).combine(gendb)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [] )
-}
-
-// Basic parameters with GenomicsDB + optional dbSNP + optional intervals
-workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
-
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    dict  = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-
-    dbsnp     = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
-    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
-
-    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.map{ it[1] }.collect()
-    gendb.add([])
-    gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
-    gendb.add([])
-
-    input = Channel.of([ id:'test' ]).combine(gendb)
-
-    GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )
-}
diff --git a/tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config b/tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
deleted file mode 100644
index 97396a74d92..00000000000
--- a/tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: GATK4_GENOTYPEGVCFS {
-        ext.prefix = { "${meta.id}.genotyped" }
-    }
-
-}
diff --git a/tests/modules/nf-core/gatk4/genotypegvcfs/test.yml b/tests/modules/nf-core/gatk4/genotypegvcfs/test.yml
deleted file mode 100644
index ac39ddfeaba..00000000000
--- a/tests/modules/nf-core/gatk4/genotypegvcfs/test.yml
+++ /dev/null
@@ -1,119 +0,0 @@
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_vcf_input
-  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_vcf_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input
-  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp
-  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_intervals
-  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals
-  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains: ["AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.05;SOR=0.693"]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input
-  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp
-  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_intervals
-  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains:
-        [
-          "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680",
-        ]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
-
-- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals
-  command: nextflow run ./tests/modules/nf-core/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/genotypegvcfs/nextflow.config
-  tags:
-    - gatk4
-    - gatk4/genotypegvcfs
-  files:
-    - path: output/gatk4/test.genotyped.vcf.gz
-      contains: ["AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.66;SOR=0.693"]
-    - path: output/gatk4/test.genotyped.vcf.gz.tbi
-    - path: output/gatk4/versions.yml