From b089ec6984bff8c33ae8931e71f6dadf21886318 Mon Sep 17 00:00:00 2001
From: manascripts <manas.sehgal@dkfz.de>
Date: Tue, 5 May 2026 11:24:00 +0200
Subject: [PATCH 1/7] Add octopusv/merge module

---
 .../nf-core/octopusv/merge/environment.yml    |  7 ++
 modules/nf-core/octopusv/merge/main.nf        | 39 ++++++++++
 modules/nf-core/octopusv/merge/meta.yml       | 72 +++++++++++++++++++
 .../nf-core/octopusv/merge/tests/main.nf.test | 69 ++++++++++++++++++
 4 files changed, 187 insertions(+)
 create mode 100644 modules/nf-core/octopusv/merge/environment.yml
 create mode 100644 modules/nf-core/octopusv/merge/main.nf
 create mode 100644 modules/nf-core/octopusv/merge/meta.yml
 create mode 100644 modules/nf-core/octopusv/merge/tests/main.nf.test

diff --git a/modules/nf-core/octopusv/merge/environment.yml b/modules/nf-core/octopusv/merge/environment.yml
new file mode 100644
index 00000000000..583655a9621
--- /dev/null
+++ b/modules/nf-core/octopusv/merge/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::octopusv=0.3.2"
diff --git a/modules/nf-core/octopusv/merge/main.nf b/modules/nf-core/octopusv/merge/main.nf
new file mode 100644
index 00000000000..e15778dba7c
--- /dev/null
+++ b/modules/nf-core/octopusv/merge/main.nf
@@ -0,0 +1,39 @@
+process OCTOPUSV_MERGE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/octopusv:0.3.2--pyhdfd78af_0' :
+        'quay.io/biocontainers/octopusv:0.3.2--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(svcfs)
+
+    output:
+    tuple val(meta), path("*.svcf"), emit: svcf
+    tuple val("${task.process}"), val('octopusv'), eval("octopusv --version"), topic: versions, emit: versions_octopusv
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    octopusv merge -i ${svcfs.join(' ')} \\
+        -o ${prefix}.svcf \\
+        ${args}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """"
+    echo $args
+
+    touch ${prefix}.svcf
+    """
+}
diff --git a/modules/nf-core/octopusv/merge/meta.yml b/modules/nf-core/octopusv/merge/meta.yml
new file mode 100644
index 00000000000..c9f2c8254e2
--- /dev/null
+++ b/modules/nf-core/octopusv/merge/meta.yml
@@ -0,0 +1,72 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+# # TODO nf-core: Add a description of the module and list keywords
+name: "octopusv_merge"
+description: "Merge and harmonize structural variant calls from multiple samples."
+keywords:
+  - structural variants
+  - merge
+  - genomics
+  - svcf
+tools:
+  - "octopusv":
+      description: "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs."
+      homepage: "https://github.com/ylab-hi/OctopuSV"
+      documentation: "https://github.com/ylab-hi/OctopuSV"
+      tool_dev_url: "https://github.com/ylab-hi/octopusV"
+      doi: "10.1093/bioinformatics/btaf599"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - svcf:
+        type: file
+        description: Sorted SVCF file
+        pattern: "*.svcf"
+        ontologies:
+          - edam: "https://github.com/ylab-hi/OctopuSV/blob/main/docs/SVCF_specifications.md" # SVCF
+
+output:
+  svcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.svcf":
+          type: file
+          description: Sorted SVCF file
+          pattern: "*.svcf"
+          ontologies:
+            - edam: "https://github.com/ylab-hi/OctopuSV/blob/main/docs/SVCF_specifications.md" # SVCF
+
+  versions_octopusv:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "octopusv":
+          type: string
+          description: The name of the tool
+      - "octopusv --version":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - octopusv:
+          type: string
+          description: The name of the tool
+      - octopusv --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@manascripts"
+maintainers:
+  - "@manascripts"
diff --git a/modules/nf-core/octopusv/merge/tests/main.nf.test b/modules/nf-core/octopusv/merge/tests/main.nf.test
new file mode 100644
index 00000000000..6bc01568690
--- /dev/null
+++ b/modules/nf-core/octopusv/merge/tests/main.nf.test
@@ -0,0 +1,69 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test octopusv/merge
+nextflow_process {
+
+    name "Test Process OCTOPUSV_MERGE"
+    script "../main.nf"
+    process "OCTOPUSV_MERGE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "octopusv"
+    tag "octopusv/merge"
+
+    test("homo_sapiens - svcf list") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'delete_me/octopusv/merge/caller1.svcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'delete_me/octopusv/merge/caller2.svcf', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.svcf.get(0).get(1)).name,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - svcf list - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/sv/octopusv/merge/caller1.svcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/sv/octopusv/merge/caller2.svcf', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+}

From db90b8c4dc7943c71e7d51c7cc2742c9f29a2383 Mon Sep 17 00:00:00 2001
From: manascripts <manas.sehgal@dkfz.de>
Date: Tue, 5 May 2026 11:29:42 +0200
Subject: [PATCH 2/7] test-data path  fix

---
 modules/nf-core/octopusv/merge/tests/main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/octopusv/merge/tests/main.nf.test b/modules/nf-core/octopusv/merge/tests/main.nf.test
index 6bc01568690..2ca89cbbb45 100644
--- a/modules/nf-core/octopusv/merge/tests/main.nf.test
+++ b/modules/nf-core/octopusv/merge/tests/main.nf.test
@@ -49,8 +49,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ],
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/sv/octopusv/merge/caller1.svcf', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/sv/octopusv/merge/caller2.svcf', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'delete_me/octopusv/merge/caller1.svcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'delete_me/octopusv/merge/caller2.svcf', checkIfExists: true)
                     ]
                 ]
                 """

From a859458783a5f1500c7c17b90aecfa1212816988 Mon Sep 17 00:00:00 2001
From: manascripts <manas.sehgal@dkfz.de>
Date: Mon, 11 May 2026 10:22:22 +0200
Subject: [PATCH 3/7] fix versioning

---
 modules/nf-core/octopusv/merge/main.nf          |  2 +-
 modules/nf-core/octopusv/merge/meta.yml         | 17 ++++++++---------
 .../nf-core/octopusv/merge/tests/main.nf.test   |  4 +---
 3 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/octopusv/merge/main.nf b/modules/nf-core/octopusv/merge/main.nf
index e15778dba7c..00e85e2729d 100644
--- a/modules/nf-core/octopusv/merge/main.nf
+++ b/modules/nf-core/octopusv/merge/main.nf
@@ -12,7 +12,7 @@ process OCTOPUSV_MERGE {
 
     output:
     tuple val(meta), path("*.svcf"), emit: svcf
-    tuple val("${task.process}"), val('octopusv'), eval("octopusv --version"), topic: versions, emit: versions_octopusv
+    tuple val("${task.process}"), val('octopusv'),  eval("python -c \"import importlib.metadata as m; print(m.version('octopusv'))\""), emit: versions_octopusv, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/octopusv/merge/meta.yml b/modules/nf-core/octopusv/merge/meta.yml
index c9f2c8254e2..fbba479fbad 100644
--- a/modules/nf-core/octopusv/merge/meta.yml
+++ b/modules/nf-core/octopusv/merge/meta.yml
@@ -25,10 +25,10 @@ input:
           e.g. `[ id:'sample1' ]`
     - svcf:
         type: file
-        description: Sorted SVCF file
+        description: Sorted VCF file
         pattern: "*.svcf"
         ontologies:
-          - edam: "https://github.com/ylab-hi/OctopuSV/blob/main/docs/SVCF_specifications.md" # SVCF
+          - edam: "http://edamontology.org/format_3016" # VCF
 
 output:
   svcf:
@@ -39,22 +39,21 @@ output:
             e.g. `[ id:'sample1' ]`
       - "*.svcf":
           type: file
-          description: Sorted SVCF file
+          description: Sorted VCF file
           pattern: "*.svcf"
           ontologies:
-            - edam: "https://github.com/ylab-hi/OctopuSV/blob/main/docs/SVCF_specifications.md" # SVCF
+            - edam: "http://edamontology.org/format_3016" # VCF
 
   versions_octopusv:
-    - - "${task.process}":
+    - - ${task.process}:
           type: string
           description: The name of the process
-      - "octopusv":
+      - octopusv:
           type: string
           description: The name of the tool
-      - "octopusv --version":
+      - python -c "import importlib.metadata as m; print(m.version('octopusv'))":
           type: eval
           description: The expression to obtain the version of the tool
-
 topics:
   versions:
     - - ${task.process}:
@@ -63,7 +62,7 @@ topics:
       - octopusv:
           type: string
           description: The name of the tool
-      - octopusv --version:
+      - python -c "import importlib.metadata as m; print(m.version('octopusv'))":
           type: eval
           description: The expression to obtain the version of the tool
 authors:
diff --git a/modules/nf-core/octopusv/merge/tests/main.nf.test b/modules/nf-core/octopusv/merge/tests/main.nf.test
index 2ca89cbbb45..c2ccb2e1eb8 100644
--- a/modules/nf-core/octopusv/merge/tests/main.nf.test
+++ b/modules/nf-core/octopusv/merge/tests/main.nf.test
@@ -1,5 +1,3 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test octopusv/merge
 nextflow_process {
 
     name "Test Process OCTOPUSV_MERGE"
@@ -31,7 +29,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    file(process.out.svcf.get(0).get(1)).name,
+                    path(process.out.svcf.get(0).get(1)).vcf.summary,
                     process.out.findAll { key, val -> key.startsWith('versions') }
                 ).match() }
             )

From 17e6b19dc38302ffd63e1ff3097c4b3c6d61deb9 Mon Sep 17 00:00:00 2001
From: manascripts <manas.sehgal@dkfz.de>
Date: Tue, 12 May 2026 15:03:15 +0200
Subject: [PATCH 4/7] add test data and update default merging logic

---
 modules/nf-core/octopusv/merge/main.nf        | 21 ++++++--
 modules/nf-core/octopusv/merge/meta.yml       | 20 ++++----
 .../nf-core/octopusv/merge/tests/main.nf.test |  9 ++--
 .../octopusv/merge/tests/main.nf.test.snap    | 48 +++++++++++++++++++
 4 files changed, 80 insertions(+), 18 deletions(-)
 create mode 100644 modules/nf-core/octopusv/merge/tests/main.nf.test.snap

diff --git a/modules/nf-core/octopusv/merge/main.nf b/modules/nf-core/octopusv/merge/main.nf
index 00e85e2729d..9249ec2e867 100644
--- a/modules/nf-core/octopusv/merge/main.nf
+++ b/modules/nf-core/octopusv/merge/main.nf
@@ -18,9 +18,24 @@ process OCTOPUSV_MERGE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args = (task.ext.args ?: '').trim()
     def prefix = task.ext.prefix ?: "${meta.id}"
 
+    def strategy_flags = [
+        '--union', '--intersect', '--specific',
+        '--min-support', '--exact-support', '--max-support', '--expression'
+    ]
+
+    def explicit_flags = strategy_flags.findAll { args.tokenize().contains(it) }
+    if (explicit_flags.size() > 1) {
+        error("OCTOPUSV_MERGE: multiple merge strategies specified: ${explicit_flags.join(', ')}")
+    }
+
+    def default_strategy = task.ext.merge_strategy ?: '--union'
+    if (explicit_flags.isEmpty()) {
+        args = "${default_strategy} ${args}".trim()
+    }
+
     """
     octopusv merge -i ${svcfs.join(' ')} \\
         -o ${prefix}.svcf \\
@@ -28,10 +43,10 @@ process OCTOPUSV_MERGE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def args = (task.ext.args ?: '').trim()
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    """"
+    """
     echo $args
 
     touch ${prefix}.svcf
diff --git a/modules/nf-core/octopusv/merge/meta.yml b/modules/nf-core/octopusv/merge/meta.yml
index fbba479fbad..1721b8136b8 100644
--- a/modules/nf-core/octopusv/merge/meta.yml
+++ b/modules/nf-core/octopusv/merge/meta.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-# # TODO nf-core: Add a description of the module and list keywords
 name: "octopusv_merge"
 description: "Merge and harmonize structural variant calls from multiple samples."
 keywords:
@@ -9,27 +7,28 @@ keywords:
   - svcf
 tools:
   - "octopusv":
-      description: "End-to-end structural variant post-processing: standardize, merge, compare, and export SVs."
+      description: "End-to-end structural variant post-processing: standardize, merge,
+        compare, and export SVs."
       homepage: "https://github.com/ylab-hi/OctopuSV"
       documentation: "https://github.com/ylab-hi/OctopuSV"
       tool_dev_url: "https://github.com/ylab-hi/octopusV"
       doi: "10.1093/bioinformatics/btaf599"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
-
 input:
   - - meta:
         type: map
         description: |
           Groovy Map containing sample information
           e.g. `[ id:'sample1' ]`
-    - svcf:
+    - svcfs:
         type: file
-        description: Sorted VCF file
+        description: List of SVCF files to merge
         pattern: "*.svcf"
         ontologies:
-          - edam: "http://edamontology.org/format_3016" # VCF
-
+          - edam: "http://edamontology.org/format_3016"
+          - edam: "http://edamontology.org/format_3615"
 output:
   svcf:
     - - meta:
@@ -42,8 +41,7 @@ output:
           description: Sorted VCF file
           pattern: "*.svcf"
           ontologies:
-            - edam: "http://edamontology.org/format_3016" # VCF
-
+            - edam: "http://edamontology.org/format_3016"
   versions_octopusv:
     - - ${task.process}:
           type: string
diff --git a/modules/nf-core/octopusv/merge/tests/main.nf.test b/modules/nf-core/octopusv/merge/tests/main.nf.test
index c2ccb2e1eb8..6a49498ea8f 100644
--- a/modules/nf-core/octopusv/merge/tests/main.nf.test
+++ b/modules/nf-core/octopusv/merge/tests/main.nf.test
@@ -17,8 +17,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ],
                     [
-                        file(params.modules_testdata_base_path + 'delete_me/octopusv/merge/caller1.svcf', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'delete_me/octopusv/merge/caller2.svcf', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/octopusv/sk-n-as-sniffles-ont.svcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/octopusv/sk-n-as-severus-ont.svcf', checkIfExists: true)
                     ]
                 ]
                 """
@@ -30,6 +30,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     path(process.out.svcf.get(0).get(1)).vcf.summary,
+                    path(process.out.svcf.get(0).get(1)).vcf.variantsMD5,
                     process.out.findAll { key, val -> key.startsWith('versions') }
                 ).match() }
             )
@@ -47,8 +48,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test' ],
                     [
-                        file(params.modules_testdata_base_path + 'delete_me/octopusv/merge/caller1.svcf', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'delete_me/octopusv/merge/caller2.svcf', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/octopusv/sk-n-as-sniffles-ont.svcf', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/octopusv/sk-n-as-severus-ont.svcf', checkIfExists: true)
                     ]
                 ]
                 """
diff --git a/modules/nf-core/octopusv/merge/tests/main.nf.test.snap b/modules/nf-core/octopusv/merge/tests/main.nf.test.snap
new file mode 100644
index 00000000000..9ecd18173fe
--- /dev/null
+++ b/modules/nf-core/octopusv/merge/tests/main.nf.test.snap
@@ -0,0 +1,48 @@
+{
+    "homo_sapiens - svcf list - stub": {
+        "content": [
+            {
+                "svcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.svcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_octopusv": [
+                    [
+                        "OCTOPUSV_MERGE",
+                        "octopusv",
+                        "0.3.2"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-12T15:01:53.694998174",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - svcf list": {
+        "content": [
+            "VcfFile [chromosomes=[chr9, chr16_KI270728v1_random, chr7, chr8, chr8_KI270816v1_alt, chrUn_KI270757v1, chr5, chr17_KI270907v1_alt, chr6, chr3, chr21, chr11, chr22, chr4, chr2_KI270772v1_alt, chr1, chr12, chr15_ML143371v1_fix, chr14, chr8_KI270901v1_alt, chr16, chr17, chr7_KI270805v1_alt], sampleCount=1, variantCount=62, phased=false, phasedAutodetect=false]",
+            "df8a9f0a3e5b517ec23ffd6ee75fd4a0",
+            {
+                "versions_octopusv": [
+                    [
+                        "OCTOPUSV_MERGE",
+                        "octopusv",
+                        "0.3.2"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-12T15:01:44.802177046",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}
\ No newline at end of file

From 601e45597b63dcd5bacc85ddfff755f38a79b535 Mon Sep 17 00:00:00 2001
From: manascripts <manas.sehgal@dkfz.de>
Date: Tue, 12 May 2026 15:39:56 +0200
Subject: [PATCH 5/7] update merge flag

---
 modules/nf-core/octopusv/merge/main.nf                 | 3 +--
 modules/nf-core/octopusv/merge/tests/main.nf.test.snap | 4 ++--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/octopusv/merge/main.nf b/modules/nf-core/octopusv/merge/main.nf
index 9249ec2e867..29926000051 100644
--- a/modules/nf-core/octopusv/merge/main.nf
+++ b/modules/nf-core/octopusv/merge/main.nf
@@ -31,9 +31,8 @@ process OCTOPUSV_MERGE {
         error("OCTOPUSV_MERGE: multiple merge strategies specified: ${explicit_flags.join(', ')}")
     }
 
-    def default_strategy = task.ext.merge_strategy ?: '--union'
     if (explicit_flags.isEmpty()) {
-        args = "${default_strategy} ${args}".trim()
+        args = "--union ${args}".trim()
     }
 
     """
diff --git a/modules/nf-core/octopusv/merge/tests/main.nf.test.snap b/modules/nf-core/octopusv/merge/tests/main.nf.test.snap
index 9ecd18173fe..7aad1874112 100644
--- a/modules/nf-core/octopusv/merge/tests/main.nf.test.snap
+++ b/modules/nf-core/octopusv/merge/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-12T15:01:53.694998174",
+        "timestamp": "2026-05-12T15:37:05.706384471",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -39,7 +39,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-12T15:01:44.802177046",
+        "timestamp": "2026-05-12T15:36:57.591463848",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

From 877cc95f4c62d52f73d588b3308bf0fa5483bae0 Mon Sep 17 00:00:00 2001
From: manascripts <manas.sehgal@dkfz.de>
Date: Tue, 12 May 2026 16:45:36 +0200
Subject: [PATCH 6/7] update tests

---
 modules/nf-core/octopusv/merge/tests/main.nf.test.snap | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/octopusv/merge/tests/main.nf.test.snap b/modules/nf-core/octopusv/merge/tests/main.nf.test.snap
index 7aad1874112..e0c41b72f00 100644
--- a/modules/nf-core/octopusv/merge/tests/main.nf.test.snap
+++ b/modules/nf-core/octopusv/merge/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-12T15:37:05.706384471",
+        "timestamp": "2026-05-12T16:45:16.948062283",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -39,7 +39,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-12T15:36:57.591463848",
+        "timestamp": "2026-05-12T16:45:08.207667648",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

From f83dbf8d81163c771a77151fc62c864e4c6db1c3 Mon Sep 17 00:00:00 2001
From: manascripts <manas.sehgal@dkfz.de>
Date: Wed, 13 May 2026 14:05:14 +0200
Subject: [PATCH 7/7] nextflow lint fixes + test update

---
 modules/nf-core/octopusv/merge/main.nf        | 19 ++++++++-----------
 .../octopusv/merge/tests/main.nf.test.snap    |  4 ++--
 2 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/octopusv/merge/main.nf b/modules/nf-core/octopusv/merge/main.nf
index 29926000051..8874a653e31 100644
--- a/modules/nf-core/octopusv/merge/main.nf
+++ b/modules/nf-core/octopusv/merge/main.nf
@@ -1,18 +1,18 @@
 process OCTOPUSV_MERGE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/octopusv:0.3.2--pyhdfd78af_0' :
-        'quay.io/biocontainers/octopusv:0.3.2--pyhdfd78af_0' }"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/octopusv:0.3.2--pyhdfd78af_0'
+        : 'quay.io/biocontainers/octopusv:0.3.2--pyhdfd78af_0'}"
 
     input:
     tuple val(meta), path(svcfs)
 
     output:
     tuple val(meta), path("*.svcf"), emit: svcf
-    tuple val("${task.process}"), val('octopusv'),  eval("python -c \"import importlib.metadata as m; print(m.version('octopusv'))\""), emit: versions_octopusv, topic: versions
+    tuple val("${task.process}"), val('octopusv'), eval("python -c \"import importlib.metadata as m; print(m.version('octopusv'))\""), emit: versions_octopusv, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,12 +21,9 @@ process OCTOPUSV_MERGE {
     def args = (task.ext.args ?: '').trim()
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def strategy_flags = [
-        '--union', '--intersect', '--specific',
-        '--min-support', '--exact-support', '--max-support', '--expression'
-    ]
+    def strategy_flags = ['--union', '--intersect', '--specific', '--min-support', '--exact-support', '--max-support', '--expression']
 
-    def explicit_flags = strategy_flags.findAll { args.tokenize().contains(it) }
+    def explicit_flags = strategy_flags.findAll { flag -> args.tokenize().contains(flag) }
     if (explicit_flags.size() > 1) {
         error("OCTOPUSV_MERGE: multiple merge strategies specified: ${explicit_flags.join(', ')}")
     }
@@ -46,7 +43,7 @@ process OCTOPUSV_MERGE {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    echo $args
+    echo ${args}
 
     touch ${prefix}.svcf
     """
diff --git a/modules/nf-core/octopusv/merge/tests/main.nf.test.snap b/modules/nf-core/octopusv/merge/tests/main.nf.test.snap
index e0c41b72f00..737dd6ec002 100644
--- a/modules/nf-core/octopusv/merge/tests/main.nf.test.snap
+++ b/modules/nf-core/octopusv/merge/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-12T16:45:16.948062283",
+        "timestamp": "2026-05-13T14:02:15.365401997",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"
@@ -39,7 +39,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-05-12T16:45:08.207667648",
+        "timestamp": "2026-05-13T14:04:02.989592821",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"