diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf
index 7c2197349dc..da54ba2cbb8 100644
--- a/modules/nf-core/delly/call/main.nf
+++ b/modules/nf-core/delly/call/main.nf
@@ -1,6 +1,6 @@
 process DELLY_CALL {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -8,14 +8,14 @@ process DELLY_CALL {
         'biocontainers/delly:1.2.6--hb7e2ac5_1' }"
 
     input:
-    tuple val(meta), path(input), path(input_index), path(vcf), path(vcf_index), path(exclude_bed)
+    tuple val(meta), path(input_1), path(input_1_idx), path(input_ctrl), path(input_ctrl_idx), path(vcf), path(vcf_index), path(exclude_bed)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
 
     output:
-    tuple val(meta), path("*.{bcf,vcf.gz}")  , emit: bcf
-    tuple val(meta), path("*.{csi,tbi}")     , emit: csi
-    path "versions.yml"                      , emit: versions
+    tuple val(meta), path("*.{bcf,vcf.gz}"), emit: bcf
+    tuple val(meta), path("*.{csi,tbi}")   , emit: csi
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,13 +23,15 @@ process DELLY_CALL {
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = task.ext.suffix ?: "bcf"
 
+    def input = input_ctrl ? "${input_1} ${input_ctrl}" : "${input_1}"
     def exclude = exclude_bed ? "--exclude ${exclude_bed}" : ""
 
     def bcf_output = suffix == "bcf" ? "--outfile ${prefix}.bcf" : ""
-    def vcf_output = suffix == "vcf" ? "| bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz && tabix ${prefix}.vcf.gz" : ""
+    def vcf_output = suffix == "vcf" ? "| bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz && tabix ${args3} ${prefix}.vcf.gz" : ""
 
     def genotype = vcf ? "--vcffile ${vcf}" : ""
 
diff --git a/modules/nf-core/delly/call/meta.yml b/modules/nf-core/delly/call/meta.yml
index cc378ffd62a..a7b08caad48 100644
--- a/modules/nf-core/delly/call/meta.yml
+++ b/modules/nf-core/delly/call/meta.yml
@@ -12,20 +12,45 @@ tools:
       documentation: https://github.com/dellytools/delly/blob/master/README.md
       doi: "10.1093/bioinformatics/bts378"
       licence: ["BSD-3-Clause"]
+      args_id: "$args"
+  - bgzip:
+      description: Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.
+      homepage: https://www.htslib.org/doc/tabix.html
+      documentation: http://www.htslib.org/doc/bgzip.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      args_id: "$args2"
+  - tabix:
+      description: Generic indexer for TAB-delimited genome position files.
+      homepage: https://www.htslib.org/doc/tabix.html
+      documentation: https://www.htslib.org/doc/tabix.1.html
+      doi: 10.1093/bioinformatics/btq671
+      licence: ["MIT"]
+      args_id: "$args3"
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - input:
+  - input_1:
       type: file
       description: BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked
       pattern: "*.{bam,cram}"
-  - input_index:
+  - input_1_idx:
       type: file
       description: Index of the BAM/CRAM file
       pattern: "*.{bai,crai}"
+  - input_ctrl:
+      type: file
+      description: |
+        Optional BAM/CRAM file of matched control sample for somatic variant calling.
+        Must be sorted, indexed, and duplicate marked.
+      pattern: "*.{bam,cram}"
+  - input_ctrl_idx:
+      type: file
+      description: Optional index of the control BAM/CRAM file
+      pattern: "*.{bai,crai}"
   - vcf:
       type: file
       description: A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped
@@ -77,6 +102,8 @@ output:
 authors:
   - "@projectoriented"
   - "@nvnieuwk"
+  - "@alexnater"
 maintainers:
   - "@projectoriented"
   - "@nvnieuwk"
+  - "@alexnater"
diff --git a/modules/nf-core/delly/call/tests/main.nf.test b/modules/nf-core/delly/call/tests/main.nf.test
index 80cad20d553..f9749ed5281 100644
--- a/modules/nf-core/delly/call/tests/main.nf.test
+++ b/modules/nf-core/delly/call/tests/main.nf.test
@@ -3,35 +3,77 @@ nextflow_process {
     name "Test Process DELLY_CALL"
     script "../main.nf"
     process "DELLY_CALL"
+    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
     tag "delly"
     tag "delly/call"
 
-    test("homo_sapiens - bam, bai, [], [], [], fasta, fai") {
+    test("germline, in:bam, out:bcf") {
+        when {
+            params {
+                suffix = 'bcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'control' ], // meta map
+                    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] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    ]
+                input[2] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
 
-        config "./vcf.config"
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
+    }
 
+    test("germline, in:bam, out:vcf") {
         when {
+            params {
+                suffix = 'vcf'
+            }
+            
             process {
                 """
                 input[0] = [
-                    [ id:'test'], // meta map
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam", checkIfExists:true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai", checkIfExists:true),
+                    [ id:'control' ], // meta map
+                    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] = [
-                    [ id:'fasta' ],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists:true)
-                ]
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    ]
                 input[2] = [
-                    [ id:'fai' ],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
-                ]
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
                 """
             }
         }
@@ -39,33 +81,42 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("bam") }
+                { assert snapshot(
+                    process.out.bcf,
+                    file(process.out.csi[0][1]).name,
+                    process.out.versions
+                    ).match()
+                },
+                { assert process.out.versions }
             )
         }
-
     }
 
-    test("homo_sapiens - cram, crai, [], [], [], fasta, fai") {
-
+    test("germline, in:cram, out:bcf") {
         when {
+            params {
+                suffix = 'bcf'
+            }
             process {
                 """
                 input[0] = [
-                    [ id:'test'], // meta map
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram", checkIfExists:true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai", checkIfExists:true),
+                    [ id:'control' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                    [],
+                    [],
                     [],
                     [],
                     []
-                ]
+                    ]
                 input[1] = [
-                    [ id:'fasta' ],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists:true)
-                ]
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
                 input[2] = [
-                    [ id:'fai' ],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
-                ]
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    ]
                 """
             }
         }
@@ -73,33 +124,81 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("cram") }
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
             )
         }
-
     }
 
-    test("homo_sapiens - cram, crai, [], [], bed, fasta, fai") {
+    test("germline, in:cram, out:vcf") {
+        when {
+            params {
+                suffix = 'vcf'
+            }
+            
+            process {
+                """
+                input[0] = [
+                    [ id:'control' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                    [],
+                    [],
+                    [],
+                    [],
+                    []
+                    ]
+                input[1] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                input[2] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.bcf,
+                    file(process.out.csi[0][1]).name,
+                    process.out.versions
+                    ).match()
+                },
+                { assert process.out.versions }
+            )
+        }
+    }
 
+    test("germline, exclude regions, in:bam, out:bcf") {
         when {
+            params {
+                suffix = 'bcf'
+            }
             process {
                 """
                 input[0] = [
-                    [ id:'test'], // meta map
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram", checkIfExists:true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai", checkIfExists:true),
+                    [ id:'control' ], // meta map
+                    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.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed", checkIfExists:true)
-                ]
+                    [],
+                    [],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+                    ]
                 input[1] = [
-                    [ id:'fasta' ],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists:true)
-                ]
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    ]
                 input[2] = [
-                    [ id:'fai' ],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
-                ]
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
                 """
             }
         }
@@ -107,32 +206,77 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("bed") }
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
             )
         }
+    }
+
+    test("germline, genotype, in:bam, out:bcf") {
+        when {
+            params {
+                suffix = 'bcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'control' ], // meta map
+                    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']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true),
+                    []
+                    ]
+                input[1] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    ]
+                input[2] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
 
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
     }
 
-    test("homo_sapiens - cram, crai, vcf, tbi, [], fasta, fai") {
+    test("germline, out:bcf - stub") {
+
+        options "-stub"
 
         when {
+            params {
+                suffix = 'bcf'
+            }
             process {
                 """
                 input[0] = [
-                    [ id:'test'], // meta map
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram", checkIfExists:true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai", checkIfExists:true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz", checkIfExists:true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi", checkIfExists:true),
+                    [ id:'test' ], // meta map
+                    [],
+                    [],
+                    [],
+                    [],
+                    [],
+                    [],
                     []
-                ]
+                    ]
                 input[1] = [
-                    [ id:'fasta' ],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists:true)
-                ]
+                    [:],
+                    []
+                    ]
                 input[2] = [
-                    [ id:'fai' ],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
+                    [:],
+                    []
                 ]
                 """
             }
@@ -141,36 +285,77 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("genotype") }
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
             )
         }
 
     }
 
-    test("homo_sapiens - bam, bai, [], [], [], fasta, fai - stub") {
+    test("somatic, in:bam, out:bcf") {
+        when {
+            params {
+                suffix = 'bcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'tumor_control' ], // meta map
+                    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] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    ]
+                input[2] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
 
-        config "./vcf.config"
-        options "-stub"
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
+    }
 
+    test("somatic, in:bam, out:vcf") {
         when {
+            params {
+                suffix = 'vcf'
+            }
+            
             process {
                 """
                 input[0] = [
-                    [ id:'test'], // meta map
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam", checkIfExists:true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai", checkIfExists:true),
+                    [ id:'tumor_control' ], // meta map
+                    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] = [
-                    [ id:'fasta' ],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta", checkIfExists:true)
-                ]
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    ]
                 input[2] = [
-                    [ id:'fai' ],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
-                ]
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
                 """
             }
         }
@@ -178,10 +363,90 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("stub") }
+                { assert snapshot(
+                    process.out.bcf,
+                    file(process.out.csi[0][1]).name,
+                    process.out.versions
+                    ).match()
+                },
+                { assert process.out.versions }
             )
         }
+    }
+
+    test("somatic, exclude regions, in:bam, out:bcf") {
+        when {
+            params {
+                suffix = 'bcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'tumor_control' ], // meta map
+                    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] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    ]
+                input[2] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
 
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
     }
 
+    test("somatic, genotype, in:bam, out:bcf") {
+        when {
+            params {
+                suffix = 'bcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'tumor_control' ], // meta map
+                    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']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true),
+                    []
+                    ]
+                input[1] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                    ]
+                input[2] = [
+                    [ id:'human' ],
+                    file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/delly/call/tests/main.nf.test.snap b/modules/nf-core/delly/call/tests/main.nf.test.snap
index c89636d9e99..d30d9d6d3d6 100644
--- a/modules/nf-core/delly/call/tests/main.nf.test.snap
+++ b/modules/nf-core/delly/call/tests/main.nf.test.snap
@@ -1,21 +1,21 @@
 {
-    "bed": {
+    "germline, exclude regions, in:bam, out:bcf": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.bcf:md5,592702d7765f246cd0f7f32f23b607b9"
+                        "control.bcf:md5,847ab56fe3d70e01857c71d7203af913"
                     ]
                 ],
                 "1": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.bcf.csi:md5,c198abfc14584c5ac69c004057927e0b"
+                        "control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
                     ]
                 ],
                 "2": [
@@ -24,17 +24,17 @@
                 "bcf": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.bcf:md5,592702d7765f246cd0f7f32f23b607b9"
+                        "control.bcf:md5,847ab56fe3d70e01857c71d7203af913"
                     ]
                 ],
                 "csi": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.bcf.csi:md5,c198abfc14584c5ac69c004057927e0b"
+                        "control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
                     ]
                 ],
                 "versions": [
@@ -44,27 +44,27 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-06T11:38:15.181069181"
+        "timestamp": "2024-04-03T15:50:51.214081941"
     },
-    "cram": {
+    "germline, genotype, in:bam, out:bcf": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.bcf:md5,592702d7765f246cd0f7f32f23b607b9"
+                        "control.bcf:md5,847ab56fe3d70e01857c71d7203af913"
                     ]
                 ],
                 "1": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.bcf.csi:md5,c198abfc14584c5ac69c004057927e0b"
+                        "control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
                     ]
                 ],
                 "2": [
@@ -73,17 +73,17 @@
                 "bcf": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.bcf:md5,592702d7765f246cd0f7f32f23b607b9"
+                        "control.bcf:md5,847ab56fe3d70e01857c71d7203af913"
                     ]
                 ],
                 "csi": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.bcf.csi:md5,c198abfc14584c5ac69c004057927e0b"
+                        "control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
                     ]
                 ],
                 "versions": [
@@ -93,27 +93,27 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-06T11:38:01.798279112"
+        "timestamp": "2024-04-03T15:51:00.5735754"
     },
-    "stub": {
+    "germline - vcf": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "control.vcf.gz:md5,1460fde017e7ab7c8aa333246475b37d"
                     ]
                 ],
                 "1": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "control.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
                     ]
                 ],
                 "2": [
@@ -122,17 +122,17 @@
                 "bcf": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "control.vcf.gz:md5,1460fde017e7ab7c8aa333246475b37d"
                     ]
                 ],
                 "csi": [
                     [
                         {
-                            "id": "test"
+                            "id": "control"
                         },
-                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "control.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
                     ]
                 ],
                 "versions": [
@@ -142,11 +142,11 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-06T11:38:44.135939928"
+        "timestamp": "2024-03-28T16:17:08.945129254"
     },
-    "bam": {
+    "germline, out:bcf - stub": {
         "content": [
             {
                 "0": [
@@ -154,7 +154,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,021dae61db384dae43a46386a66d1408"
+                        "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -162,7 +162,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                        "test.bcf.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
@@ -173,7 +173,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,021dae61db384dae43a46386a66d1408"
+                        "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "csi": [
@@ -181,7 +181,511 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                        "test.bcf.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-02T14:38:32.89939847"
+    },
+    "somatic - vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.vcf.gz:md5,761d7f427a4f8119343d1aab1d3f5642"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.vcf.gz:md5,761d7f427a4f8119343d1aab1d3f5642"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-28T16:17:43.10253227"
+    },
+    "germline, in:bam, out:vcf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "control"
+                    },
+                    "control.vcf.gz:md5,681158f860e9aa801c197b5ebf4742eb"
+                ]
+            ],
+            "control.vcf.gz.tbi",
+            [
+                "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-03T15:50:28.605707686"
+    },
+    "germline - bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf:md5,6e2d79f69afc702a08511cb929da6943"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf:md5,6e2d79f69afc702a08511cb929da6943"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-28T16:16:59.976411614"
+    },
+    "germline, in:cram, out:bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf:md5,fb284989139b6b7a86049dc7f084e462"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf.csi:md5,a2ba4f0b32a6ea857ec8a5b3068f168f"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf:md5,fb284989139b6b7a86049dc7f084e462"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf.csi:md5,a2ba4f0b32a6ea857ec8a5b3068f168f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-03T15:50:36.531751261"
+    },
+    "somatic, in:bam, out:bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf:md5,9f15c148df32709a67e0bf44d6c704ba"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf:md5,9f15c148df32709a67e0bf44d6c704ba"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-03T15:51:22.461691094"
+    },
+    "somatic - bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf:md5,ab52d577db09a1e500607c124eacf511"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf:md5,ab52d577db09a1e500607c124eacf511"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-28T16:17:32.903383226"
+    },
+    "germline, in:cram, out:vcf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "control"
+                    },
+                    "control.vcf.gz:md5,42c4f91d40334139ea56a9c0e0824f41"
+                ]
+            ],
+            "control.vcf.gz.tbi",
+            [
+                "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-03T15:50:43.580758846"
+    },
+    "germline, in:bam, out:bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf:md5,847ab56fe3d70e01857c71d7203af913"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf:md5,847ab56fe3d70e01857c71d7203af913"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-03T15:50:19.100132232"
+    },
+    "germline - genotyping": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf:md5,6e2d79f69afc702a08511cb929da6943"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf:md5,6e2d79f69afc702a08511cb929da6943"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-28T16:51:43.202596735"
+    },
+    "somatic, in:bam, out:vcf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "tumor_control"
+                    },
+                    "tumor_control.vcf.gz:md5,10ada5fa3a46dfaf59a87959354ac392"
+                ]
+            ],
+            "tumor_control.vcf.gz.tbi",
+            [
+                "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-03T15:51:31.81185897"
+    },
+    "somatic, exclude regions, in:bam, out:bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf:md5,9f15c148df32709a67e0bf44d6c704ba"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf:md5,9f15c148df32709a67e0bf44d6c704ba"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-03T15:51:40.61756269"
+    },
+    "somatic, genotype, in:bam, out:bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf:md5,9f15c148df32709a67e0bf44d6c704ba"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,cf72d737ee881a7cd7eab87abf93b94c"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf:md5,9f15c148df32709a67e0bf44d6c704ba"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
                     ]
                 ],
                 "versions": [
@@ -191,11 +695,11 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-06T11:37:45.689766253"
+        "timestamp": "2024-04-03T15:51:50.44863729"
     },
-    "genotype": {
+    "germline - stub": {
         "content": [
             {
                 "0": [
@@ -203,7 +707,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,592702d7765f246cd0f7f32f23b607b9"
+                        "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -211,7 +715,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf.csi:md5,c198abfc14584c5ac69c004057927e0b"
+                        "test.bcf.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
@@ -222,7 +726,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,592702d7765f246cd0f7f32f23b607b9"
+                        "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "csi": [
@@ -230,7 +734,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf.csi:md5,c198abfc14584c5ac69c004057927e0b"
+                        "test.bcf.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -240,8 +744,8 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-06T11:38:29.129594523"
+        "timestamp": "2024-03-21T16:54:36.024035492"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/delly/call/tests/nextflow.config b/modules/nf-core/delly/call/tests/nextflow.config
new file mode 100644
index 00000000000..ae81082b359
--- /dev/null
+++ b/modules/nf-core/delly/call/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+
+    withName: DELLY_CALL {
+        ext.suffix = { params.suffix ?: '' }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/delly/filter/environment.yml b/modules/nf-core/delly/filter/environment.yml
new file mode 100644
index 00000000000..1b073fdfe7b
--- /dev/null
+++ b/modules/nf-core/delly/filter/environment.yml
@@ -0,0 +1,7 @@
+name: delly_filter
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::delly=1.2.6
diff --git a/modules/nf-core/delly/filter/main.nf b/modules/nf-core/delly/filter/main.nf
new file mode 100644
index 00000000000..f27017f512e
--- /dev/null
+++ b/modules/nf-core/delly/filter/main.nf
@@ -0,0 +1,84 @@
+process DELLY_FILTER {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/delly:1.2.6--hb7e2ac5_0':
+        'biocontainers/delly:1.2.6--hb7e2ac5_0' }"
+
+    input:
+    tuple val(meta), path(bcf), path(csi)
+    val(mode)
+    path(samples)
+    val(tumor_samples)
+    val(control_samples)
+
+    output:
+    tuple val(meta), path("${prefix}.{bcf,vcf.gz}")        , emit: bcf
+    tuple val(meta), path("${prefix}.{bcf.csi,vcf.gz.tbi}"), emit: csi
+    path "versions.yml"                                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.suffix ?: "bcf"
+    if ("$bcf" == "${prefix}.${suffix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    def samples_arg = ''
+    def sample_list = ''
+    if (mode == 'somatic') {
+        if (!samples && tumor_samples && control_samples) {
+            sample_list = tumor_samples.collect {"${it}\ttumor"}.join('\n')
+            sample_list += '\n' + control_samples.collect {"${it}\tcontrol"}.join('\n')
+        }
+        else {
+            error "For somatic mode, either lists of sample ids for tumor and control samples or a sample description file must be provided."
+        }
+        samples_arg = '-s samples.tsv'
+    } else if (mode != 'germline') {
+        error "Mode must be one of 'germline' or 'somatic'."
+    }
+
+    bcf_output = suffix == "bcf" ? "--outfile ${prefix}.bcf" : ""
+    vcf_output = suffix == "vcf" ? "| bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz && tabix ${args3} ${prefix}.vcf.gz" : ""
+
+    """
+    if [ "$samples_arg" ]; then echo "$sample_list" > samples.tsv; fi
+
+    delly \\
+        filter \\
+        $args \\
+        -f $mode \\
+        $bcf_output \\
+        $samples_arg \\
+        $bcf \\
+        $vcf_output
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        delly: \$( echo \$(delly --version 2>&1) | sed 's/^.*Delly version: v//; s/ using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.suffix ?: "bcf"
+
+    def bcf_output = suffix == "bcf" ? "touch ${prefix}.bcf && touch ${prefix}.bcf.csi" : ""
+    def vcf_output = suffix == "vcf" ? "touch ${prefix}.vcf.gz && touch ${prefix}.vcf.gz.tbi" : ""
+
+    """
+    ${bcf_output}
+    ${vcf_output}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        delly: \$( echo \$(delly --version 2>&1) | sed 's/^.*Delly version: v//; s/ using.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/delly/filter/meta.yml b/modules/nf-core/delly/filter/meta.yml
new file mode 100644
index 00000000000..38b648ecd5e
--- /dev/null
+++ b/modules/nf-core/delly/filter/meta.yml
@@ -0,0 +1,89 @@
+name: delly_filter
+description: Filter structural variants
+keywords:
+  - genome
+  - structural
+  - variants
+  - bcf
+tools:
+  - delly:
+      description: Structural variant discovery by integrated paired-end and split-read analysis
+      homepage: https://github.com/dellytools/delly
+      documentation: https://github.com/dellytools/delly/blob/master/README.md
+      doi: "10.1093/bioinformatics/bts378"
+      licence: ["BSD-3-Clause"]
+      args_id: "$args"
+  - bgzip:
+      description: Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.
+      homepage: https://www.htslib.org/doc/tabix.html
+      documentation: http://www.htslib.org/doc/bgzip.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      args_id: "$args2"
+  - tabix:
+      description: Generic indexer for TAB-delimited genome position files.
+      homepage: https://www.htslib.org/doc/tabix.html
+      documentation: https://www.htslib.org/doc/tabix.1.html
+      doi: 10.1093/bioinformatics/btq671
+      licence: ["MIT"]
+      args_id: "$args3"
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bcf:
+      type: file
+      description: BCF file with structural variants
+      pattern: "*.bcf"
+  - csi:
+      type: file
+      description: A csi index that matches the bcf input
+      pattern: "*.bcf.csi"
+  - mode:
+      type: string
+      description: The working mode of Delly filter
+      pattern: "germline|somatic"
+  - samples:
+      type: file
+      description: |
+        A TSV sample description file where the first column
+        is sample id (matching sample names in the BCF file)
+        and the second column is either tumor or control.
+        Only needed for somatic mode. Alternatively, sample desciptions
+        can be added the meta map as lists of sample ids in the
+        fields 'tumor_samples' and 'control_samples'.
+      pattern: "*.tsv"
+  - tumor_samples:
+      type: list
+      description: |
+        List of sample ids for tumor samples (matching sample names in the BCF file).
+        Only needed for somatic mode and if no sample description file is provided.
+  - control_samples:
+      type: list
+      description: |
+        List of sample ids for control samples (matching sample names in the BCF file).
+        Only needed for somatic mode and if no sample description file is provided.
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'sample1', single_end:false ]
+  - bcf:
+      type: file
+      description: Filtered variants in BCF format
+      pattern: "*.bcf"
+  - csi:
+      type: file
+      description: A generated csi index that matches the bcf output
+      pattern: "*.bcf.csi"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@alexnater"
+maintainers:
+  - "@alexnater"
diff --git a/modules/nf-core/delly/filter/tests/main.nf.test b/modules/nf-core/delly/filter/tests/main.nf.test
new file mode 100644
index 00000000000..1b5364f57d5
--- /dev/null
+++ b/modules/nf-core/delly/filter/tests/main.nf.test
@@ -0,0 +1,270 @@
+nextflow_process {
+
+    name "Test Process DELLY_FILTER"
+    script "../main.nf"
+    process "DELLY_FILTER"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "delly"
+    tag "delly/call"
+    tag "delly/filter"
+
+    test("germline, out:bcf") {
+        setup {
+            run("DELLY_CALL") {
+                script "../../call/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'control' ], // meta map
+                        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] = [
+                        [ id:'human' ],
+                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        ]
+                    input[2] = [
+                        [ id:'human' ],
+                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                        ]
+                    """
+                }
+            }
+        }
+
+        when {
+            params {
+                suffix = 'bcf'
+            }
+            process {
+                """
+                input[0] = DELLY_CALL.out.bcf.join(DELLY_CALL.out.csi)
+                input[1] = "germline"
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
+    }
+
+    test("germline, out:vcf") {
+        setup {
+            run("DELLY_CALL") {
+                script "../../call/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'control' ], // meta map
+                        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] = [
+                        [ id:'human' ],
+                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        ]
+                    input[2] = [
+                        [ id:'human' ],
+                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                        ]
+                    """
+                }
+            }
+        }
+
+        when {
+            params {
+                suffix = 'vcf'
+            }
+            process {
+                """
+                input[0] = DELLY_CALL.out.bcf.join(DELLY_CALL.out.csi)
+                input[1] = "germline"
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.bcf,
+                    file(process.out.csi[0][1]).name,
+                    process.out.versions
+                    ).match()
+                },
+                { assert process.out.versions }
+            )
+        }
+    }
+
+    test("germline, out:bcf - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                suffix = 'bcf'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [],
+                    []
+                    ]
+                input[1] = "germline"
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
+
+    }
+
+    test("somatic, out:bcf") {
+        setup {
+            run("DELLY_CALL") {
+                script "../../call/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'tumor_control' ], // meta map
+                        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] = [
+                        [ id:'human' ],
+                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        ]
+                    input[2] = [
+                        [ id:'human' ],
+                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                        ]
+                    """
+                }
+            }
+        }
+        when {
+            params {
+                suffix = 'bcf'
+            }
+            process {
+                """
+                ch_input = DELLY_CALL.out.bcf
+                            .join(DELLY_CALL.out.csi)
+                input[0] = ch_input
+                input[1] = "somatic"
+                input[2] = []
+                input[3] = ['tumour']
+                input[4] = ['normal']
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert process.out.versions }
+            )
+        }
+    }
+
+    test("somatic, out:vcf") {
+        setup {
+            run("DELLY_CALL") {
+                script "../../call/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'tumor_control' ], // meta map
+                        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] = [
+                        [ id:'human' ],
+                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                        ]
+                    input[2] = [
+                        [ id:'human' ],
+                        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+                        ]
+                    """
+                }
+            }
+        }
+        when {
+            params {
+                suffix = 'vcf'
+            }
+            process {
+                """
+                ch_input = DELLY_CALL.out.bcf
+                            .join(DELLY_CALL.out.csi)
+                input[0] = ch_input
+                input[1] = "somatic"
+                input[2] = []
+                input[3] = ['tumour']
+                input[4] = ['normal']
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.bcf,
+                    file(process.out.csi[0][1]).name,
+                    process.out.versions
+                    ).match()
+                },
+                { assert process.out.versions }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/delly/filter/tests/main.nf.test.snap b/modules/nf-core/delly/filter/tests/main.nf.test.snap
new file mode 100644
index 00000000000..e287d50f631
--- /dev/null
+++ b/modules/nf-core/delly/filter/tests/main.nf.test.snap
@@ -0,0 +1,436 @@
+{
+    "germline - vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.vcf.gz:md5,5ad9b88451652e7016f868afff34663d"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f45104c406e3750e1f09c3ead45a8829"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.vcf.gz:md5,5ad9b88451652e7016f868afff34663d"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f45104c406e3750e1f09c3ead45a8829"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-28T17:12:10.446267262"
+    },
+    "germline, out:vcf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "control"
+                    },
+                    "control.filtered.vcf.gz:md5,ea9954c30161573c866117e9c270543f"
+                ]
+            ],
+            "control.filtered.vcf.gz.tbi",
+            [
+                "versions.yml:md5,f45104c406e3750e1f09c3ead45a8829"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-03T16:52:24.481427707"
+    },
+    "somatic - bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.bcf:md5,95aa415128c8e9806e3415f9e2598e4a"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f67ef5fd2fa49a82ccea58f0d3d5ad0f"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.bcf:md5,95aa415128c8e9806e3415f9e2598e4a"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f67ef5fd2fa49a82ccea58f0d3d5ad0f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-28T17:01:49.506842172"
+    },
+    "germline, out:bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.bcf:md5,9e59a224ae0be4d2fa07c3742b4143dc"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f45104c406e3750e1f09c3ead45a8829"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.bcf:md5,9e59a224ae0be4d2fa07c3742b4143dc"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f45104c406e3750e1f09c3ead45a8829"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-03T16:52:13.714416817"
+    },
+    "germline, out:bcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.bcf.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f45104c406e3750e1f09c3ead45a8829"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.bcf.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f45104c406e3750e1f09c3ead45a8829"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-02T15:01:00.391495451"
+    },
+    "somatic, out:bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.bcf:md5,6ddf6991c652e7a8728363c901fa728b"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f67ef5fd2fa49a82ccea58f0d3d5ad0f"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.bcf:md5,6ddf6991c652e7a8728363c901fa728b"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f67ef5fd2fa49a82ccea58f0d3d5ad0f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-03T16:52:42.486375101"
+    },
+    "somatic - vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.vcf.gz:md5,462cf52ecf899b3e5fa29beacaf15eb6"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f67ef5fd2fa49a82ccea58f0d3d5ad0f"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.vcf.gz:md5,462cf52ecf899b3e5fa29beacaf15eb6"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "tumor_control"
+                        },
+                        "tumor_control.filtered.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f67ef5fd2fa49a82ccea58f0d3d5ad0f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-28T17:15:30.448939231"
+    },
+    "somatic, out:vcf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "tumor_control"
+                    },
+                    "tumor_control.filtered.vcf.gz:md5,a85a88fec57b657d9fed01e2a65199e4"
+                ]
+            ],
+            "tumor_control.filtered.vcf.gz.tbi",
+            [
+                "versions.yml:md5,f67ef5fd2fa49a82ccea58f0d3d5ad0f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-03T16:52:53.78719012"
+    },
+    "germline - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.bcf.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f45104c406e3750e1f09c3ead45a8829"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.bcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.bcf.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f45104c406e3750e1f09c3ead45a8829"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-21T17:17:18.241522976"
+    },
+    "germline - bcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.bcf:md5,e34200aa9681cfa2ffd4d62aa7714c70"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f45104c406e3750e1f09c3ead45a8829"
+                ],
+                "bcf": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.bcf:md5,e34200aa9681cfa2ffd4d62aa7714c70"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "control"
+                        },
+                        "control.filtered.bcf.csi:md5,66545c77fc791a02dadc7fc252d04635"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f45104c406e3750e1f09c3ead45a8829"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-28T17:07:24.711897762"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/delly/filter/tests/nextflow.config b/modules/nf-core/delly/filter/tests/nextflow.config
new file mode 100644
index 00000000000..8b440dbd88a
--- /dev/null
+++ b/modules/nf-core/delly/filter/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: DELLY_FILTER {
+        ext.prefix = { "${meta.id}.filtered" }
+        ext.suffix = { params.suffix ?: '' }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/delly/filter/tests/tags.yml b/modules/nf-core/delly/filter/tests/tags.yml
new file mode 100644
index 00000000000..5acc4a869d6
--- /dev/null
+++ b/modules/nf-core/delly/filter/tests/tags.yml
@@ -0,0 +1,2 @@
+delly/filter:
+  - "modules/nf-core/delly/filter/**"