Add new module: octopusv/stat

modules/nf-core/octopusv/stat/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=0.3.3"

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

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+process OCTOPUSV_STAT {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/octopusv:0.3.3--pyhdfd78af_0' :
+        'quay.io/biocontainers/octopusv:0.3.3--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(svcf)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: txt
+    tuple val(meta), path("*.html"), emit: html, optional: true
+    tuple val("${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 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    octopusv stat \\
+        ${svcf} \\
+        --output-file ${prefix}.txt \\
+        ${args}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo $args
+
+    touch ${prefix}.txt
+    """
+}

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

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+name: "octopusv_stat"
+description: Summarize structural variant statistics from octopusv SVCF files
+keywords:
+  - vcf summary
+  - structural variant
+  - statistics
+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: SVCF file from octopusv
+        pattern: "*.svcf"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016"
+output:
+  txt:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.txt":
+          type: file
+          description: A TXT file containing the statistics of the structural
+            variants in the input VCF
+          pattern: "*.txt"
+          ontologies:
+            - edam: "http://edamontology.org/format_2330"
+  html:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.html":
+          type: file
+          description: An HTML report with SV statistics
+          pattern: "*.html"
+          ontologies:
+            - edam: "http://edamontology.org/format_2331"
+  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/stat/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process OCTOPUSV_STAT"
+    script "../main.nf"
+    process "OCTOPUSV_STAT"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "octopusv"
+    tag "octopusv/stat"
+
+    test("homo_sapiens - txt + html") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    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 file(process.out.html.get(0).get(1)).name == "test.html" },
+                { assert snapshot(
+                    process.out.txt,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - txt - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    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/stat/tests/main.nf.test.snap

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+{
+    "homo_sapiens - txt + html": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.txt:md5,8ecae13307448ee0c11882909f554507"
+                ]
+            ],
+            {
+                "versions_octopusv": [
+                    [
+                        "OCTOPUSV_STAT",
+                        "octopusv",
+                        "0.3.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-26T17:05:05.640088507",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "homo_sapiens - txt - stub": {
+        "content": [
+            {
+                "html": [
+
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_octopusv": [
+                    [
+                        "OCTOPUSV_STAT",
+                        "octopusv",
+                        "0.3.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-26T17:05:12.720177373",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    }
+}

modules/nf-core/octopusv/stat/tests/nextflow.config

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+process {
+  withName: 'OCTOPUSV_STAT' {
+    ext.args = "--report"
+  }
+}