From d30f78f9d4d3f562c0d07fc4c91af2d80d53e279 Mon Sep 17 00:00:00 2001
From: Andrea Bagnacani <andrea.bagnacani@limbus-medtec.com>
Date: Fri, 27 Mar 2026 23:08:19 +0100
Subject: [PATCH 1/6] Bump delly version

---
 modules/nf-core/delly/call/environment.yml    |  2 +-
 modules/nf-core/delly/call/main.nf            |  4 +--
 .../delly/call/tests/main.nf.test.snap        | 28 +++++++++----------
 3 files changed, 17 insertions(+), 17 deletions(-)

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..87b94f66f981 100644
--- a/modules/nf-core/delly/call/main.nf
+++ b/modules/nf-core/delly/call/main.nf
@@ -4,8 +4,8 @@ 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)
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..3d3c38947fc0 100644
--- a/modules/nf-core/delly/call/tests/main.nf.test.snap
+++ b/modules/nf-core/delly/call/tests/main.nf.test.snap
@@ -22,12 +22,12 @@
                     [
                         "DELLY_CALL",
                         "delly",
-                        "1.3.3"
+                        "1.7.3"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-19T16:50:15.628255934",
+        "timestamp": "2026-03-27T22:51:54.216495545",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -41,7 +41,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,85e9ba0873366c41099bddf72d4ebe4e"
+                        "test.bcf:md5,de0ac784efa4da9ecd236d4e9b9e99df"
                     ]
                 ],
                 "csi": [
@@ -56,12 +56,12 @@
                     [
                         "DELLY_CALL",
                         "delly",
-                        "1.3.3"
+                        "1.7.3"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-19T16:50:05.300001721",
+        "timestamp": "2026-03-27T22:51:33.931579498",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -75,7 +75,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,85e9ba0873366c41099bddf72d4ebe4e"
+                        "test.bcf:md5,de0ac784efa4da9ecd236d4e9b9e99df"
                     ]
                 ],
                 "csi": [
@@ -90,12 +90,12 @@
                     [
                         "DELLY_CALL",
                         "delly",
-                        "1.3.3"
+                        "1.7.3"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-19T16:49:48.55960664",
+        "timestamp": "2026-03-27T22:50:57.395295355",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -109,7 +109,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,85e9ba0873366c41099bddf72d4ebe4e"
+                        "test.bcf:md5,de0ac784efa4da9ecd236d4e9b9e99df"
                     ]
                 ],
                 "csi": [
@@ -124,12 +124,12 @@
                     [
                         "DELLY_CALL",
                         "delly",
-                        "1.3.3"
+                        "1.7.3"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-19T16:49:56.887027305",
+        "timestamp": "2026-03-27T22:51:14.902129068",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -143,7 +143,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,3d655b3f166bb13a993b608d58c71183"
+                        "test.vcf.gz:md5,e030fce4d07043b1b1101238394f0b58"
                     ]
                 ],
                 "csi": [
@@ -158,12 +158,12 @@
                     [
                         "DELLY_CALL",
                         "delly",
-                        "1.3.3"
+                        "1.7.3"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-02-19T16:49:39.279196351",
+        "timestamp": "2026-03-27T22:50:35.147896323",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"

From 92a5a79bbc1b6956329cb3f938d41e13cb9399a4 Mon Sep 17 00:00:00 2001
From: Andrea Bagnacani <andrea.bagnacani@limbus-medtec.com>
Date: Fri, 27 Mar 2026 23:53:28 +0100
Subject: [PATCH 2/6] Make use of threads

---
 modules/nf-core/delly/call/main.nf            |  1 +
 modules/nf-core/delly/call/tests/cpus.config  |  5 ++
 modules/nf-core/delly/call/tests/main.nf.test | 35 +++++++++++++
 .../delly/call/tests/main.nf.test.snap        | 50 ++++++++++++++++---
 4 files changed, 83 insertions(+), 8 deletions(-)
 create mode 100644 modules/nf-core/delly/call/tests/cpus.config

diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf
index 87b94f66f981..06f8341f024d 100644
--- a/modules/nf-core/delly/call/main.nf
+++ b/modules/nf-core/delly/call/main.nf
@@ -37,6 +37,7 @@ process DELLY_CALL {
     delly \\
         call \\
         ${args} \\
+        --threads ${task.cpus} \\
         ${bcf_output} \\
         --genome ${fasta} \\
         ${genotype} \\
diff --git a/modules/nf-core/delly/call/tests/cpus.config b/modules/nf-core/delly/call/tests/cpus.config
new file mode 100644
index 000000000000..38ceec37363d
--- /dev/null
+++ b/modules/nf-core/delly/call/tests/cpus.config
@@ -0,0 +1,5 @@
+process {
+    withName: "DELLY_CALL" {
+        cpus = 2
+    }
+}
diff --git a/modules/nf-core/delly/call/tests/main.nf.test b/modules/nf-core/delly/call/tests/main.nf.test
index 23b3bb3fa803..87949322cd3a 100644
--- a/modules/nf-core/delly/call/tests/main.nf.test
+++ b/modules/nf-core/delly/call/tests/main.nf.test
@@ -45,6 +45,41 @@ nextflow_process {
 
     }
 
+    test("homo_sapiens - bam, bai, [], [], [], fasta, fai - cpus") {
+
+        config "./cpus.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)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
     test("homo_sapiens - cram, crai, [], [], [], fasta, fai") {
 
         when {
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 3d3c38947fc0..272244ed8b5f 100644
--- a/modules/nf-core/delly/call/tests/main.nf.test.snap
+++ b/modules/nf-core/delly/call/tests/main.nf.test.snap
@@ -41,7 +41,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,de0ac784efa4da9ecd236d4e9b9e99df"
+                        "test.bcf:md5,5322c86bb993f438e82854deea22b3b7"
                     ]
                 ],
                 "csi": [
@@ -61,7 +61,41 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T22:51:33.931579498",
+        "timestamp": "2026-03-30T09:11:24.6958461",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - bam, bai, [], [], [], fasta, fai - cpus": {
+        "content": [
+            {
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,5322c86bb993f438e82854deea22b3b7"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf.csi:md5,c198abfc14584c5ac69c004057927e0b"
+                    ]
+                ],
+                "versions_delly": [
+                    [
+                        "DELLY_CALL",
+                        "delly",
+                        "1.7.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-30T09:10:06.363073",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -75,7 +109,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,de0ac784efa4da9ecd236d4e9b9e99df"
+                        "test.bcf:md5,5322c86bb993f438e82854deea22b3b7"
                     ]
                 ],
                 "csi": [
@@ -95,7 +129,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T22:50:57.395295355",
+        "timestamp": "2026-03-30T09:10:31.258243552",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -109,7 +143,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,de0ac784efa4da9ecd236d4e9b9e99df"
+                        "test.bcf:md5,5322c86bb993f438e82854deea22b3b7"
                     ]
                 ],
                 "csi": [
@@ -129,7 +163,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T22:51:14.902129068",
+        "timestamp": "2026-03-30T09:10:57.489937033",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -143,7 +177,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,e030fce4d07043b1b1101238394f0b58"
+                        "test.vcf.gz:md5,57ab0bbd0b2d1fdeae15b73fde5ea11b"
                     ]
                 ],
                 "csi": [
@@ -163,7 +197,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T22:50:35.147896323",
+        "timestamp": "2026-03-30T09:09:33.602234165",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"

From 86979c9a66293547c0fefc4a28a08d861f25f373 Mon Sep 17 00:00:00 2001
From: Andrea Bagnacani <andrea.bagnacani@limbus-medtec.com>
Date: Mon, 30 Mar 2026 20:39:16 +0200
Subject: [PATCH 3/6] Replace unallowed key

---
 modules/nf-core/delly/call/main.nf          | 12 ++++++------
 modules/nf-core/delly/call/meta.yml         |  4 ++--
 modules/nf-core/delly/call/tests/vcf.config |  2 +-
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf
index 06f8341f024d..7b8583207983 100644
--- a/modules/nf-core/delly/call/main.nf
+++ b/modules/nf-core/delly/call/main.nf
@@ -23,13 +23,13 @@ process DELLY_CALL {
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: "bcf"
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = task.ext.suffix ?: "bcf"
 
     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 bcf_output = args3 == "bcf" ? "--outfile ${prefix}.bcf" : ""
+    def vcf_output = args3 == "vcf" ? "| bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz && tabix ${prefix}.vcf.gz" : ""
 
     def genotype = vcf ? "--vcffile ${vcf}" : ""
 
@@ -47,11 +47,11 @@ process DELLY_CALL {
     """
 
     stub:
+    def args3 = task.ext.args3 ?: "bcf"
     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" : ""
+    def bcf_output = args3 == "bcf" ? "touch ${prefix}.bcf && touch ${prefix}.bcf.csi" : ""
+    def vcf_output = args3 == "vcf" ? "echo '' | gzip > ${prefix}.vcf.gz && touch ${prefix}.vcf.gz.tbi" : ""
 
     """
     ${bcf_output}
diff --git a/modules/nf-core/delly/call/meta.yml b/modules/nf-core/delly/call/meta.yml
index e62d98b17fb8..82bc93bc0338 100644
--- a/modules/nf-core/delly/call/meta.yml
+++ b/modules/nf-core/delly/call/meta.yml
@@ -78,8 +78,8 @@ 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. Specify either "bcf"
+            or "vcf" in ext.args3 to define the output type
           pattern: "*.{bcf,vcf.gz}"
           ontologies: []
   csi:
diff --git a/modules/nf-core/delly/call/tests/vcf.config b/modules/nf-core/delly/call/tests/vcf.config
index eba4419bd50b..bdbf6318972a 100644
--- a/modules/nf-core/delly/call/tests/vcf.config
+++ b/modules/nf-core/delly/call/tests/vcf.config
@@ -1,5 +1,5 @@
 process {
     withName: "DELLY_CALL" {
-        ext.suffix = "vcf"
+        ext.args3 = "vcf"
     }
 }

From a35613440cd41bde6e271082c65275132d7797f3 Mon Sep 17 00:00:00 2001
From: Andrea Bagnacani <andrea.bagnacani@limbus-medtec.com>
Date: Tue, 31 Mar 2026 23:36:39 +0200
Subject: [PATCH 4/6] Create dedicated vcf/bcf channel

---
 modules/nf-core/delly/call/main.nf  | 11 +++++------
 modules/nf-core/delly/call/meta.yml | 11 +++++++++--
 2 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/modules/nf-core/delly/call/main.nf b/modules/nf-core/delly/call/main.nf
index 7b8583207983..05df82b25bbc 100644
--- a/modules/nf-core/delly/call/main.nf
+++ b/modules/nf-core/delly/call/main.nf
@@ -11,6 +11,7 @@ process DELLY_CALL {
     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
@@ -23,13 +24,12 @@ process DELLY_CALL {
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
-    def args3 = task.ext.args3 ?: "bcf"
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     def exclude = exclude_bed ? "--exclude ${exclude_bed}" : ""
 
-    def bcf_output = args3 == "bcf" ? "--outfile ${prefix}.bcf" : ""
-    def vcf_output = args3 == "vcf" ? "| bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz && tabix ${prefix}.vcf.gz" : ""
+    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 genotype = vcf ? "--vcffile ${vcf}" : ""
 
@@ -47,11 +47,10 @@ process DELLY_CALL {
     """
 
     stub:
-    def args3 = task.ext.args3 ?: "bcf"
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def bcf_output = args3 == "bcf" ? "touch ${prefix}.bcf && touch ${prefix}.bcf.csi" : ""
-    def vcf_output = args3 == "vcf" ? "echo '' | gzip > ${prefix}.vcf.gz && touch ${prefix}.vcf.gz.tbi" : ""
+    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" : ""
 
     """
     ${bcf_output}
diff --git a/modules/nf-core/delly/call/meta.yml b/modules/nf-core/delly/call/meta.yml
index 82bc93bc0338..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.args3 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:

From 50795d2218b69c388b61ce96bdd3223b8a621496 Mon Sep 17 00:00:00 2001
From: Andrea Bagnacani <andrea.bagnacani@limbus-medtec.com>
Date: Tue, 31 Mar 2026 23:37:50 +0200
Subject: [PATCH 5/6] Adapt tests to new vcf/bcf channel

---
 modules/nf-core/delly/call/tests/main.nf.test | 88 +++++++++++++++++--
 .../delly/call/tests/main.nf.test.snap        | 68 ++++++++++----
 .../tests/{cpus.config => nextflow.config}    |  0
 modules/nf-core/delly/call/tests/vcf.config   |  5 --
 4 files changed, 130 insertions(+), 31 deletions(-)
 rename modules/nf-core/delly/call/tests/{cpus.config => nextflow.config} (100%)
 delete mode 100644 modules/nf-core/delly/call/tests/vcf.config

diff --git a/modules/nf-core/delly/call/tests/main.nf.test b/modules/nf-core/delly/call/tests/main.nf.test
index 87949322cd3a..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'
                 """
             }
         }
@@ -42,12 +76,44 @@ 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 - cpus") {
+    test("homo_sapiens - bam, bai, [], [], [], fasta, fai, bcf - config") {
 
-        config "./cpus.config"
+        config "./nextflow.config"
 
         when {
             process {
@@ -68,6 +134,7 @@ nextflow_process {
                     [ id:'fai' ],
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists:true)
                 ]
+                input[3] = 'bcf'
                 """
             }
         }
@@ -80,7 +147,7 @@ nextflow_process {
         }
     }
 
-    test("homo_sapiens - cram, crai, [], [], [], fasta, fai") {
+    test("homo_sapiens - cram, crai, [], [], [], fasta, fai, bcf") {
 
         when {
             process {
@@ -101,6 +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'
                 """
             }
         }
@@ -114,7 +182,7 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - cram, crai, [], [], bed, fasta, fai") {
+    test("homo_sapiens - cram, crai, [], [], bed, fasta, fai, bcf") {
 
         when {
             process {
@@ -135,6 +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'
                 """
             }
         }
@@ -148,7 +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 {
@@ -169,6 +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'
                 """
             }
         }
@@ -182,9 +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 {
@@ -206,6 +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 272244ed8b5f..badd9c860487 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": [
@@ -27,13 +27,13 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T22:51:54.216495545",
+        "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:md5,5322c86bb993f438e82854deea22b3b7"
+                        "test.bcf:md5,3642b5547d36e66f19f7b0c0a7237e4d"
                     ]
                 ],
                 "csi": [
@@ -61,13 +61,13 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-30T09:11:24.6958461",
+        "timestamp": "2026-03-31T23:18:56.286832808",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
         }
     },
-    "homo_sapiens - bam, bai, [], [], [], fasta, fai - cpus": {
+    "homo_sapiens - bam, bai, [], [], [], fasta, fai, bcf": {
         "content": [
             {
                 "bcf": [
@@ -75,7 +75,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,5322c86bb993f438e82854deea22b3b7"
+                        "test.bcf:md5,3642b5547d36e66f19f7b0c0a7237e4d"
                     ]
                 ],
                 "csi": [
@@ -95,13 +95,13 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-30T09:10:06.363073",
+        "timestamp": "2026-03-31T23:14:00.829431804",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
         }
     },
-    "homo_sapiens - cram, crai, [], [], [], fasta, fai": {
+    "homo_sapiens - cram, crai, vcf, tbi, [], fasta, fai, bcf": {
         "content": [
             {
                 "bcf": [
@@ -109,7 +109,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,5322c86bb993f438e82854deea22b3b7"
+                        "test.bcf:md5,3642b5547d36e66f19f7b0c0a7237e4d"
                     ]
                 ],
                 "csi": [
@@ -129,13 +129,13 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-30T09:10:31.258243552",
+        "timestamp": "2026-03-31T22:56:36.491484544",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
         }
     },
-    "homo_sapiens - cram, crai, [], [], bed, fasta, fai": {
+    "homo_sapiens - bam, bai, [], [], [], fasta, fai, bcf - config": {
         "content": [
             {
                 "bcf": [
@@ -143,7 +143,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,5322c86bb993f438e82854deea22b3b7"
+                        "test.bcf:md5,3642b5547d36e66f19f7b0c0a7237e4d"
                     ]
                 ],
                 "csi": [
@@ -163,13 +163,13 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-30T09:10:57.489937033",
+        "timestamp": "2026-03-31T23:18:37.748722475",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
         }
     },
-    "homo_sapiens - bam, bai, [], [], [], fasta, fai": {
+    "homo_sapiens - bam, bai, [], [], [], fasta, fai, vcf": {
         "content": [
             {
                 "bcf": [
@@ -177,7 +177,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,57ab0bbd0b2d1fdeae15b73fde5ea11b"
+                        "test.vcf.gz:md5,df28a58e2982f86bc9e326a90cc041de"
                     ]
                 ],
                 "csi": [
@@ -197,7 +197,41 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-30T09:09:33.602234165",
+        "timestamp": "2026-03-31T22:55:15.603436593",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - cram, crai, [], [], bed, fasta, fai, bcf": {
+        "content": [
+            {
+                "bcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf:md5,3642b5547d36e66f19f7b0c0a7237e4d"
+                    ]
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bcf.csi:md5,c198abfc14584c5ac69c004057927e0b"
+                    ]
+                ],
+                "versions_delly": [
+                    [
+                        "DELLY_CALL",
+                        "delly",
+                        "1.7.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-31T22:56:14.331610098",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
diff --git a/modules/nf-core/delly/call/tests/cpus.config b/modules/nf-core/delly/call/tests/nextflow.config
similarity index 100%
rename from modules/nf-core/delly/call/tests/cpus.config
rename to modules/nf-core/delly/call/tests/nextflow.config
diff --git a/modules/nf-core/delly/call/tests/vcf.config b/modules/nf-core/delly/call/tests/vcf.config
deleted file mode 100644
index bdbf6318972a..000000000000
--- a/modules/nf-core/delly/call/tests/vcf.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: "DELLY_CALL" {
-        ext.args3 = "vcf"
-    }
-}

From 0627d31ef8513bdfc5f5f4c8534f234f2837357a Mon Sep 17 00:00:00 2001
From: Andrea Bagnacani <andrea.bagnacani@limbus-medtec.com>
Date: Wed, 1 Apr 2026 09:41:32 +0200
Subject: [PATCH 6/6] Update test snapshot

---
 .../delly/call/tests/main.nf.test.snap        | 24 +++++++++----------
 1 file changed, 12 insertions(+), 12 deletions(-)

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 badd9c860487..be29257837b3 100644
--- a/modules/nf-core/delly/call/tests/main.nf.test.snap
+++ b/modules/nf-core/delly/call/tests/main.nf.test.snap
@@ -41,7 +41,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,3642b5547d36e66f19f7b0c0a7237e4d"
+                        "test.bcf:md5,9d9ef4d09622ee9460401e49dcaf398d"
                     ]
                 ],
                 "csi": [
@@ -61,7 +61,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T23:18:56.286832808",
+        "timestamp": "2026-04-01T08:45:04.964142647",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -75,7 +75,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,3642b5547d36e66f19f7b0c0a7237e4d"
+                        "test.bcf:md5,9d9ef4d09622ee9460401e49dcaf398d"
                     ]
                 ],
                 "csi": [
@@ -95,7 +95,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T23:14:00.829431804",
+        "timestamp": "2026-04-01T08:43:58.870564235",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -109,7 +109,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,3642b5547d36e66f19f7b0c0a7237e4d"
+                        "test.bcf:md5,9d9ef4d09622ee9460401e49dcaf398d"
                     ]
                 ],
                 "csi": [
@@ -129,7 +129,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T22:56:36.491484544",
+        "timestamp": "2026-04-01T08:45:42.65724177",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -143,7 +143,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,3642b5547d36e66f19f7b0c0a7237e4d"
+                        "test.bcf:md5,9d9ef4d09622ee9460401e49dcaf398d"
                     ]
                 ],
                 "csi": [
@@ -163,7 +163,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T23:18:37.748722475",
+        "timestamp": "2026-04-01T08:44:43.856518328",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -177,7 +177,7 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,df28a58e2982f86bc9e326a90cc041de"
+                        "test.vcf.gz:md5,49c63c62559827d8b47e5d64d30a1e83"
                     ]
                 ],
                 "csi": [
@@ -197,7 +197,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T22:55:15.603436593",
+        "timestamp": "2026-04-01T08:43:36.727290615",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -211,7 +211,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bcf:md5,3642b5547d36e66f19f7b0c0a7237e4d"
+                        "test.bcf:md5,9d9ef4d09622ee9460401e49dcaf398d"
                     ]
                 ],
                 "csi": [
@@ -231,7 +231,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T22:56:14.331610098",
+        "timestamp": "2026-04-01T08:45:23.053857188",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"