diff --git a/.github/conda_skip.yml b/.github/conda_skip.yml
index 14da877f04d..8e7683a4d55 100644
--- a/.github/conda_skip.yml
+++ b/.github/conda_skip.yml
@@ -182,5 +182,7 @@ exclude:
     path: modules/nf-core/xeniumranger/resegment
   - profile: conda
     path: modules/nf-core/xeniumranger/import-segmentation
+  - profile: conda
+    path: modules/nf-core/parabricks/indexgvcf
   - profile: conda
     path: modules/nf-core/parabricks/genotypegvcf
diff --git a/modules/nf-core/parabricks/indexgvcf/main.nf b/modules/nf-core/parabricks/indexgvcf/main.nf
index bc082fca255..378f3a8b88b 100644
--- a/modules/nf-core/parabricks/indexgvcf/main.nf
+++ b/modules/nf-core/parabricks/indexgvcf/main.nf
@@ -1,16 +1,17 @@
 process PARABRICKS_INDEXGVCF {
     tag "$meta.id"
     label 'process_high'
+    label 'process_gpu'
+    stageInMode 'copy' // needed by the module to work properly - might be removed when this is 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(gvcf, stageAs:'')
+    tuple val(meta), path(gvcf)
 
     output:
-    // This tool outputs g.vcf.idx if input is uncompressed, g.vcf.gz.tbi if input is compressed
-    tuple val(meta), path("*.g.vcf*") , emit: gvcf_index
-    path "versions.yml"               , emit: versions
+    tuple val(meta), path("*.{idx,tbi}") , emit: gvcf_index
+    path "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,12 +22,12 @@ process PARABRICKS_INDEXGVCF {
         error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
+    def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
     """
     pbrun \\
         indexgvcf \\
         --input $gvcf \\
+        $num_gpus \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
@@ -39,19 +40,10 @@ process PARABRICKS_INDEXGVCF {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
+    def output_cmd = gvcf.any{ it.name.endsWith(".gz") } ? "touch ${prefix}.g.vcf.gz.tbi" : "touch ${prefix}.g.vcf.idx"
     """
-    # Different outputs generated depending if file is gzipped
-    case $gvcf in
-    *.gz )
-        touch ${prefix}.g.vcf.gz.tbi
-        ;;
-    * )
-        touch ${prefix}.g.vcf.idx
-        ;;
-    esac
+    $output_cmd
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/parabricks/indexgvcf/meta.yml b/modules/nf-core/parabricks/indexgvcf/meta.yml
index be57547075a..bc0e277660a 100644
--- a/modules/nf-core/parabricks/indexgvcf/meta.yml
+++ b/modules/nf-core/parabricks/indexgvcf/meta.yml
@@ -30,9 +30,11 @@ output:
           type: map
           description: |
             Groovy Map containing output information
-      - "*.g.vcf*":
-          type: file
-          description: Indexed gvcf file
+          pattern: "*.g.vcf"
+      - "*.{idx,tbi}":
+          type: map
+          description: |
+            Groovy Map containing output information
           pattern: "*.g.vcf"
   - versions:
       - versions.yml:
diff --git a/modules/nf-core/parabricks/indexgvcf/tests/main.nf.test b/modules/nf-core/parabricks/indexgvcf/tests/main.nf.test
new file mode 100644
index 00000000000..a6c0c79946e
--- /dev/null
+++ b/modules/nf-core/parabricks/indexgvcf/tests/main.nf.test
@@ -0,0 +1,109 @@
+nextflow_process {
+
+    name "Test Process PARABRICKS_INDEXGVCF"
+    script "../main.nf"
+    process "PARABRICKS_INDEXGVCF"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "parabricks"
+    tag "parabricks/indexgvcf"
+    tag "gpu"
+
+    test("human - gvcf") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.gvcf_index[0][1]).name,
+                    process.out.versions
+                    ).match() 
+                }
+            )
+        }
+
+    }
+
+    test("human - gvcf.gz") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("human - gvcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("human - gvcf.gz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/parabricks/indexgvcf/tests/main.nf.test.snap b/modules/nf-core/parabricks/indexgvcf/tests/main.nf.test.snap
new file mode 100644
index 00000000000..e25496cc885
--- /dev/null
+++ b/modules/nf-core/parabricks/indexgvcf/tests/main.nf.test.snap
@@ -0,0 +1,114 @@
+{
+    "human - gvcf.gz": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.genome.g.vcf.gz.tbi:md5,a581ec2827af89dbe82d09951c1725ec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ],
+                "gvcf_index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.genome.g.vcf.gz.tbi:md5,a581ec2827af89dbe82d09951c1725ec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T10:16:48.994612337"
+    },
+    "human - gvcf": {
+        "content": [
+            "test.genome.g.vcf.idx",
+            [
+                "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T10:21:20.010561875"
+    },
+    "human - gvcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.g.vcf.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ],
+                "gvcf_index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.g.vcf.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T10:21:32.292223281"
+    },
+    "human - gvcf.gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ],
+                "gvcf_index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a6c2622b9fd9223dbc349c2a27e9a2e4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T10:14:58.744532337"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 65451e16eb6..adfddd44dad 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -401,9 +401,6 @@ parabricks/deepvariant:
 parabricks/haplotypecaller:
   - modules/nf-core/parabricks/haplotypecaller/**
   - tests/modules/nf-core/parabricks/haplotypecaller/**
-parabricks/indexgvcf:
-  - modules/nf-core/parabricks/indexgvcf/**
-  - tests/modules/nf-core/parabricks/indexgvcf/**
 parabricks/mutectcaller:
   - modules/nf-core/parabricks/mutectcaller/**
   - tests/modules/nf-core/parabricks/mutectcaller/**
diff --git a/tests/modules/nf-core/parabricks/indexgvcf/main.nf b/tests/modules/nf-core/parabricks/indexgvcf/main.nf
deleted file mode 100644
index 0be4206915d..00000000000
--- a/tests/modules/nf-core/parabricks/indexgvcf/main.nf
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PARABRICKS_INDEXGVCF } from '../../../../../modules/nf-core/parabricks/indexgvcf/main.nf'
-
-workflow test_parabricks_indexgvcf {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
-    ]
-
-    process stage {
-    input:
-    tuple val(meta), path(gvcf)
-
-    output:
-    tuple val(meta), path("*.g.vcf")
-
-    script:
-    """
-    mv $gvcf test.genome.g.vcf
-    """
-    }
-
-    PARABRICKS_INDEXGVCF ( stage ( input ) )
-}
-
-workflow test_parabricks_indexgvcf_gz {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true)
-    ]
-
-    process stage_gz {
-    stageInMode "copy"
-
-    input:
-    tuple val(meta), path(gvcf)
-
-    output:
-    tuple val(meta), path("*.g.vcf.gz")
-
-    script:
-    """
-    mv $gvcf test.genome.g.vcf.gz
-    """
-    }
-
-    PARABRICKS_INDEXGVCF ( stage_gz ( input ) )
-}
diff --git a/tests/modules/nf-core/parabricks/indexgvcf/nextflow.config b/tests/modules/nf-core/parabricks/indexgvcf/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/parabricks/indexgvcf/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/parabricks/indexgvcf/test.yml b/tests/modules/nf-core/parabricks/indexgvcf/test.yml
deleted file mode 100644
index d13fd56c4b1..00000000000
--- a/tests/modules/nf-core/parabricks/indexgvcf/test.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: parabricks indexgvcf test_parabricks_indexgvcf
-  command: nextflow run ./tests/modules/nf-core/parabricks/indexgvcf -entry test_parabricks_indexgvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/indexgvcf/nextflow.config -stub-run
-  tags:
-    - parabricks
-    - parabricks/indexgvcf
-  files:
-    - path: output/parabricks/test.g.vcf.idx
-      should_exist: true
-    - path: output/parabricks/versions.yml
-
-- name: parabricks indexgvcf test_parabricks_indexgvcf_gz
-  command: nextflow run ./tests/modules/nf-core/parabricks/indexgvcf -entry test_parabricks_indexgvcf_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/indexgvcf/nextflow.config -stub-run
-  tags:
-    - parabricks
-    - parabricks/indexgvcf
-  files:
-    - path: output/parabricks/test.g.vcf.gz.tbi
-      should_exist: true
-    - path: output/parabricks/versions.yml
diff --git a/tests/modules/nf-core/parabricks/indexgvcf/test_GPU_config.txt b/tests/modules/nf-core/parabricks/indexgvcf/test_GPU_config.txt
deleted file mode 100644
index 7d5cca922bd..00000000000
--- a/tests/modules/nf-core/parabricks/indexgvcf/test_GPU_config.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    memory = "15.GB"
-    cpus  = 4
-    accelerator = 1
-}
-docker.runOptions = "--gpus all"
-singularity.runOptions = "--nv"
diff --git a/tests/modules/nf-core/parabricks/indexgvcf/test_GPU_yml.txt b/tests/modules/nf-core/parabricks/indexgvcf/test_GPU_yml.txt
deleted file mode 100644
index fde28ba6cd0..00000000000
--- a/tests/modules/nf-core/parabricks/indexgvcf/test_GPU_yml.txt
+++ /dev/null
@@ -1,19 +0,0 @@
-- name: parabricks indexgvcf test_parabricks_indexgvcf
-  command: nextflow run ./tests/modules/nf-core/parabricks/indexgvcf -entry test_parabricks_indexgvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/indexgvcf/test_GPU_config.txt
-  tags:
-    - parabricks
-    - parabricks/indexgvcf
-  files:
-    - path: output/parabricks/test.g.vcf.idx
-      md5sum: 40eef3bc2d5cd28b576d3db308674a1d
-    - path: output/parabricks/versions.yml
-
-- name: parabricks indexgvcf test_parabricks_indexgvcf_gz
-  command: nextflow run ./tests/modules/nf-core/parabricks/indexgvcf -entry test_parabricks_indexgvcf_gz -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/indexgvcf/test_GPU_config.txt
-  tags:
-    - parabricks
-    - parabricks/indexgvcf
-  files:
-    - path: output/parabricks/test.g.vcf.gz.tbi
-      md5sum: a581ec2827af89dbe82d09951c1725ec
-    - path: output/parabricks/versions.yml