diff --git a/modules/nf-core/delly/call/environment.yml b/modules/nf-core/delly/call/environment.yml
index db3a41ec8ccf..d3495af95e05 100644
--- a/modules/nf-core/delly/call/environment.yml
+++ b/modules/nf-core/delly/call/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::delly=1.3.3
+  - bioconda::delly=1.7.3
diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf
index cffa1985849f..05df82b25bbc 100644
--- a/modules/nf-core/delly/call/main.nf
+++ b/modules/nf-core/delly/call/main.nf
@@ -4,13 +4,14 @@ process DELLY_CALL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/delly:1.3.3--h4d20210_0' :
-        'biocontainers/delly:1.3.3--h4d20210_0' }"
+        'https://depot.galaxyproject.org/singularity/delly:1.7.3--hd6466ae_0' :
+        'biocontainers/delly:1.7.3--hd6466ae_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(vcf), path(vcf_index), path(exclude_bed)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
+    val(suffix)
 
     output:
     tuple val(meta), path("*.{bcf,vcf.gz}")  , emit: bcf
@@ -24,7 +25,6 @@ process DELLY_CALL {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = task.ext.suffix ?: "bcf"
 
     def exclude = exclude_bed ? "--exclude ${exclude_bed}" : ""
 
@@ -37,6 +37,7 @@ process DELLY_CALL {
     delly \\
         call \\
         ${args} \\
+        --threads ${task.cpus} \\
         ${bcf_output} \\
         --genome ${fasta} \\
         ${genotype} \\
@@ -47,7 +48,6 @@ process DELLY_CALL {
 
     stub:
     def 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" ? "echo '' | gzip > ${prefix}.vcf.gz && touch ${prefix}.vcf.gz.tbi" : ""
diff --git a/modules/nf-core/delly/call/meta.yml b/modules/nf-core/delly/call/meta.yml
index e62d98b17fb8..cc5e7f9c5334 100644
--- a/modules/nf-core/delly/call/meta.yml
+++ b/modules/nf-core/delly/call/meta.yml
@@ -69,6 +69,13 @@ input:
         description: Index of reference fasta file to identify split-reads
         pattern: "*.fai"
         ontologies: []
+  - suffix:
+      type: string
+      description: A flag to specify whether the output should be in BCF or VCF
+        format
+      enum:
+        - "bcf"
+        - "vcf"
 output:
   bcf:
     - - meta:
@@ -78,8 +85,8 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.{bcf,vcf.gz}":
           type: file
-          description: Called variants in BCF/VCF format. Specify either "bcf" or
-            "vcf" in ext.suffix to define the output type
+          description: Called variants in BCF/VCF format. Set suffix to either
+            "bcf" or "vcf" to define the output type
           pattern: "*.{bcf,vcf.gz}"
           ontologies: []
   csi:
diff --git a/modules/nf-core/delly/call/tests/main.nf.test b/modules/nf-core/delly/call/tests/main.nf.test
index 23b3bb3fa803..9d05a4bda0e9 100644
--- a/modules/nf-core/delly/call/tests/main.nf.test
+++ b/modules/nf-core/delly/call/tests/main.nf.test
@@ -9,9 +9,42 @@ nextflow_process {
     tag "delly"
     tag "delly/call"
 
-    test("homo_sapiens - bam, bai, [], [], [], fasta, fai") {
+    test("homo_sapiens - bam, bai, [], [], [], fasta, fai, vcf") {
 
-        config "./vcf.config"
+        when {
+            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),
+                    [],
+                    [],
+                    []
+                ]
+                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)
+                ]
+                input[3] = 'vcf'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - bam, bai, [], [], [], fasta, fai, bcf") {
 
         when {
             process {
@@ -32,6 +65,7 @@ nextflow_process {
                     [ id:'fai' ],
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
                 ]
+                input[3] = 'bcf'
                 """
             }
         }
@@ -42,10 +76,78 @@ nextflow_process {
                 { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
+    }
+
+    test("homo_sapiens - bam, bai, [], [], [], fasta, fai, []") {
+
+        when {
+            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),
+                    [],
+                    [],
+                    []
+                ]
+                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)
+                ]
+                input[3] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert !process.success },
+            )
+        }
+    }
+
+    test("homo_sapiens - bam, bai, [], [], [], fasta, fai, bcf - config") {
+
+        config "./nextflow.config"
 
+        when {
+            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),
+                    [],
+                    [],
+                    []
+                ]
+                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)
+                ]
+                input[3] = 'bcf'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
     }
 
-    test("homo_sapiens - cram, crai, [], [], [], fasta, fai") {
+    test("homo_sapiens - cram, crai, [], [], [], fasta, fai, bcf") {
 
         when {
             process {
@@ -66,6 +168,7 @@ nextflow_process {
                     [ id:'fai' ],
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
                 ]
+                input[3] = 'bcf'
                 """
             }
         }
@@ -79,7 +182,7 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - cram, crai, [], [], bed, fasta, fai") {
+    test("homo_sapiens - cram, crai, [], [], bed, fasta, fai, bcf") {
 
         when {
             process {
@@ -100,6 +203,7 @@ nextflow_process {
                     [ id:'fai' ],
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
                 ]
+                input[3] = 'bcf'
                 """
             }
         }
@@ -113,7 +217,7 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - cram, crai, vcf, tbi, [], fasta, fai") {
+    test("homo_sapiens - cram, crai, vcf, tbi, [], fasta, fai, bcf") {
 
         when {
             process {
@@ -134,6 +238,7 @@ nextflow_process {
                     [ id:'fai' ],
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
                 ]
+                input[3] = 'bcf'
                 """
             }
         }
@@ -147,9 +252,8 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - bam, bai, [], [], [], fasta, fai - stub") {
+    test("homo_sapiens - bam, bai, [], [], [], fasta, fai, vcf - stub") {
 
-        config "./vcf.config"
         options "-stub"
 
         when {
@@ -171,6 +275,7 @@ nextflow_process {
                     [ id:'fai' ],
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
                 ]
+                input[3] = 'vcf'
                 """
             }
         }
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 edcafa3901f0..be29257837b3 100644
--- a/modules/nf-core/delly/call/tests/main.nf.test.snap
+++ b/modules/nf-core/delly/call/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "homo_sapiens - bam, bai, [], [], [], fasta, fai - stub": {
+    "homo_sapiens - bam, bai, [], [], [], fasta, fai, vcf - stub": {
         "content": [
             {
                 "bcf": [
@@ -22,18 +22,18 @@
                     [
                         "DELLY_CALL",
                         "delly",
-                        "1.3.3"
+                        "1.7.3"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-19T16:50:15.628255934",
+        "timestamp": "2026-03-31T22:56:56.675286386",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
         }
     },
-    "homo_sapiens - cram, crai, vcf, tbi, [], fasta, fai": {
+    "homo_sapiens - cram, crai, [], [], [], fasta, fai, bcf": {
         "content": [
             {
                 "bcf": [
@@ -41,7 +41,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,85e9ba0873366c41099bddf72d4ebe4e"
+                        "test.bcf:md5,9d9ef4d09622ee9460401e49dcaf398d"
                     ]
                 ],
                 "csi": [
@@ -56,18 +56,18 @@
                     [
                         "DELLY_CALL",
                         "delly",
-                        "1.3.3"
+                        "1.7.3"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-19T16:50:05.300001721",
+        "timestamp": "2026-04-01T08:45:04.964142647",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
         }
     },
-    "homo_sapiens - cram, crai, [], [], [], fasta, fai": {
+    "homo_sapiens - bam, bai, [], [], [], fasta, fai, bcf": {
         "content": [
             {
                 "bcf": [
@@ -75,7 +75,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,85e9ba0873366c41099bddf72d4ebe4e"
+                        "test.bcf:md5,9d9ef4d09622ee9460401e49dcaf398d"
                     ]
                 ],
                 "csi": [
@@ -90,18 +90,18 @@
                     [
                         "DELLY_CALL",
                         "delly",
-                        "1.3.3"
+                        "1.7.3"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-19T16:49:48.55960664",
+        "timestamp": "2026-04-01T08:43:58.870564235",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
         }
     },
-    "homo_sapiens - cram, crai, [], [], bed, fasta, fai": {
+    "homo_sapiens - cram, crai, vcf, tbi, [], fasta, fai, bcf": {
         "content": [
             {
                 "bcf": [
@@ -109,7 +109,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,85e9ba0873366c41099bddf72d4ebe4e"
+                        "test.bcf:md5,9d9ef4d09622ee9460401e49dcaf398d"
                     ]
                 ],
                 "csi": [
@@ -124,18 +124,18 @@
                     [
                         "DELLY_CALL",
                         "delly",
-                        "1.3.3"
+                        "1.7.3"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-19T16:49:56.887027305",
+        "timestamp": "2026-04-01T08:45:42.65724177",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
         }
     },
-    "homo_sapiens - bam, bai, [], [], [], fasta, fai": {
+    "homo_sapiens - bam, bai, [], [], [], fasta, fai, bcf - config": {
         "content": [
             {
                 "bcf": [
@@ -143,7 +143,41 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,3d655b3f166bb13a993b608d58c71183"
+                        "test.bcf:md5,9d9ef4d09622ee9460401e49dcaf398d"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf.csi:md5,c198abfc14584c5ac69c004057927e0b"
+                    ]
+                ],
+                "versions_delly": [
+                    [
+                        "DELLY_CALL",
+                        "delly",
+                        "1.7.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-01T08:44:43.856518328",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - bam, bai, [], [], [], fasta, fai, vcf": {
+        "content": [
+            {
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,49c63c62559827d8b47e5d64d30a1e83"
                     ]
                 ],
                 "csi": [
@@ -158,12 +192,46 @@
                     [
                         "DELLY_CALL",
                         "delly",
-                        "1.3.3"
+                        "1.7.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-01T08:43:36.727290615",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - cram, crai, [], [], bed, fasta, fai, bcf": {
+        "content": [
+            {
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,9d9ef4d09622ee9460401e49dcaf398d"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf.csi:md5,c198abfc14584c5ac69c004057927e0b"
+                    ]
+                ],
+                "versions_delly": [
+                    [
+                        "DELLY_CALL",
+                        "delly",
+                        "1.7.3"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-19T16:49:39.279196351",
+        "timestamp": "2026-04-01T08:45:23.053857188",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
diff --git a/modules/nf-core/delly/call/tests/vcf.config b/modules/nf-core/delly/call/tests/nextflow.config
similarity index 63%
rename from modules/nf-core/delly/call/tests/vcf.config
rename to modules/nf-core/delly/call/tests/nextflow.config
index eba4419bd50b..38ceec37363d 100644
--- a/modules/nf-core/delly/call/tests/vcf.config
+++ b/modules/nf-core/delly/call/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
     withName: "DELLY_CALL" {
-        ext.suffix = "vcf"
+        cpus = 2
     }
 }