diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf
index eb86b9b8d9c..191f04995df 100644
--- a/modules/nf-core/glnexus/main.nf
+++ b/modules/nf-core/glnexus/main.nf
@@ -1,6 +1,6 @@
 process GLNEXUS {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -9,6 +9,7 @@ process GLNEXUS {
 
     input:
     tuple val(meta), path(gvcfs)
+    tuple val(meta2), path(bed)
 
     output:
     tuple val(meta), path("*.bcf"), emit: bcf
@@ -20,6 +21,7 @@ process GLNEXUS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def regions = bed ? "--bed ${bed}" : ""
 
     // Make list of GVCFs to merge
     def input = gvcfs.collect { it.toString() }
@@ -33,6 +35,7 @@ process GLNEXUS {
     glnexus_cli \\
         --threads $task.cpus \\
         --mem-gbytes $avail_mem \\
+        $regions \\
         $args \\
         ${input.join(' ')} \\
         > ${prefix}.bcf
diff --git a/modules/nf-core/glnexus/meta.yml b/modules/nf-core/glnexus/meta.yml
index a79fc63cff3..8f18bf3f871 100644
--- a/modules/nf-core/glnexus/meta.yml
+++ b/modules/nf-core/glnexus/meta.yml
@@ -23,6 +23,15 @@ input:
         type: list
         description: Input genomic vcf files
         pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing regions information
+          e.g. [ id:'test' ]
+    - bed:
+        type: list
+        description: Input BED file
+        pattern: "*.bed"
 output:
   - bcf:
       - meta:
diff --git a/modules/nf-core/glnexus/tests/main.nf.test b/modules/nf-core/glnexus/tests/main.nf.test
new file mode 100644
index 00000000000..79f7adc868d
--- /dev/null
+++ b/modules/nf-core/glnexus/tests/main.nf.test
@@ -0,0 +1,97 @@
+nextflow_process {
+
+    name "Test Process GLNEXUS"
+    script "../main.nf"
+    process "GLNEXUS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "glnexus"
+
+    test("vcfs, []") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ 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/test2.genome.vcf.gz', checkIfExists: true),
+                    ]
+                ])
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("vcfs, bed") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ 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/test2.genome.vcf.gz', checkIfExists: true),
+                    ]
+                ])
+                input[1] = [
+                    [ id:'region' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("vcfs, bed - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ 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/test2.genome.vcf.gz', checkIfExists: true),
+                    ]
+                ])
+                input[1] = [
+                    [ id:'region' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/glnexus/tests/main.nf.test.snap b/modules/nf-core/glnexus/tests/main.nf.test.snap
new file mode 100644
index 00000000000..3d2e13f09d9
--- /dev/null
+++ b/modules/nf-core/glnexus/tests/main.nf.test.snap
@@ -0,0 +1,101 @@
+{
+    "vcfs, bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T12:17:01.253378301"
+    },
+    "vcfs, bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T12:16:53.859544065"
+    },
+    "vcfs, []": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-29T12:13:03.068397129"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 0bf3c88fbc6..832f747e594 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -263,9 +263,6 @@ gfastats:
 gget/gget:
   - modules/nf-core/gget/gget/**
   - tests/modules/nf-core/gget/gget/**
-glnexus:
-  - modules/nf-core/glnexus/**
-  - tests/modules/nf-core/glnexus/**
 gprofiler2/gost:
   - modules/nf-core/gprofiler2/gost/**
   - tests/modules/nf-core/gprofiler2/gost/**
diff --git a/tests/modules/nf-core/glnexus/main.nf b/tests/modules/nf-core/glnexus/main.nf
deleted file mode 100644
index 86debecc4ab..00000000000
--- a/tests/modules/nf-core/glnexus/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GLNEXUS } from '../../../../modules/nf-core/glnexus/main.nf'
-
-workflow test_glnexus {
-    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']['test2_genome_vcf_gz'], checkIfExists: true)
-        ]
-    ]
-
-    GLNEXUS ( input )
-}
diff --git a/tests/modules/nf-core/glnexus/nextflow.config b/tests/modules/nf-core/glnexus/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/glnexus/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/glnexus/test.yml b/tests/modules/nf-core/glnexus/test.yml
deleted file mode 100644
index b8ed6751541..00000000000
--- a/tests/modules/nf-core/glnexus/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: glnexus test_glnexus
-  command: nextflow run ./tests/modules/nf-core/glnexus -entry test_glnexus -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/glnexus/nextflow.config
-  tags:
-    - glnexus
-  files:
-    - path: output/glnexus/test.bcf
-      md5sum: 62b2cea9c1b92ac63645cb031eea46fc