New module: octopusv/merge

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"

modules/nf-core/octopusv/merge/main.nf

@@ -0,0 +1,50 @@
+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("python -c \"import importlib.metadata as m; print(m.version('octopusv'))\""), emit: versions_octopusv, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    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 { flag -> args.tokenize().contains(flag) }
+    if (explicit_flags.size() > 1) {
+        error("OCTOPUSV_MERGE: multiple merge strategies specified: ${explicit_flags.join(', ')}")
+    }
+
+    if (explicit_flags.isEmpty()) {
+        args = "--union ${args}".trim()
+    }
+
+    """
+    octopusv merge -i ${svcfs.join(' ')} \\
+        -o ${prefix}.svcf \\
+        ${args}
+    """
+
+    stub:
+    def args = (task.ext.args ?: '').trim()
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo ${args}
+
+    touch ${prefix}.svcf
+    """
+}

modules/nf-core/octopusv/merge/meta.yml

@@ -0,0 +1,69 @@
+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' ]`
+    - svcfs:
+        type: file
+        description: List of SVCF files to merge
+        pattern: "*.svcf"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016"
+          - edam: "http://edamontology.org/format_3615"
+output:
+  svcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.svcf":
+          type: file
+          description: Sorted VCF file
+          pattern: "*.svcf"
+          ontologies:
+            - edam: "http://edamontology.org/format_3016"
+  versions_octopusv:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - octopusv:
+          type: string
+          description: The name of the tool
+      - 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}:
+          type: string
+          description: The name of the process
+      - octopusv:
+          type: string
+          description: The name of the tool
+      - python -c "import importlib.metadata as m; print(m.version('octopusv'))":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@manascripts"
+maintainers:
+  - "@manascripts"

modules/nf-core/octopusv/merge/tests/main.nf.test

@@ -0,0 +1,68 @@
+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 + '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)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { 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() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - svcf list - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        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)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+}

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": "2026-05-13T14:02:15.365401997",
+        "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": "2026-05-13T14:04:02.989592821",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}