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Add new module: octopusv/plot (#11747)
* Add new module: octopusv/plot * update test * update tests * Update modules/nf-core/octopusv/plot/main.nf --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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‎modules/nf-core/octopusv/plot/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- "bioconda::octopusv=0.3.3"

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

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process OCTOPUSV_PLOT {
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tag "${meta.id}"
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label 'process_single'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
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? 'https://depot.galaxyproject.org/singularity/octopusv:0.3.3--pyhdfd78af_0'
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: 'quay.io/biocontainers/octopusv:0.3.3--pyhdfd78af_0'}"
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input:
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tuple val(meta), path(txt)
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output:
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tuple val(meta), path("${prefix}_sv_sizes.png"), emit: sv_sizes_png
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tuple val(meta), path("${prefix}_sv_sizes.svg"), emit: sv_sizes_svg
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tuple val(meta), path("${prefix}_sv_types.png"), emit: sv_types_png
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tuple val(meta), path("${prefix}_sv_types.svg"), emit: sv_types_svg
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tuple val(meta), path("${prefix}_chromosome_distribution.png"), emit: chromosome_distribution_png
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tuple val(meta), path("${prefix}_chromosome_distribution.svg"), emit: chromosome_distribution_svg
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tuple val("${task.process}"), val('octopusv'), eval("python -c \"import importlib.metadata as m; print(m.version('octopusv'))\""), emit: versions_octopusv, topic: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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octopusv plot \\
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${txt} \\
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--output-prefix ${prefix} \\
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${args}
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"""
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stub:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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echo ${args}
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touch ${prefix}_sv_sizes.svg
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touch ${prefix}_sv_sizes.png
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touch ${prefix}_sv_types.png
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touch ${prefix}_sv_types.svg
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touch ${prefix}_chromosome_distribution.png
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touch ${prefix}_chromosome_distribution.svg
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"""
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}

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

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
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name: "octopusv_plot"
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description: "Plot structural variant statistics using octopusv stat output"
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keywords:
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- summary
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- structural variant
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- statistics
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- plot
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tools:
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- "octopusv":
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description: "End-to-end structural variant post-processing: standardize, merge,
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compare, and export SVs."
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homepage: "https://github.com/ylab-hi/OctopuSV"
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documentation: "https://github.com/ylab-hi/OctopuSV"
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tool_dev_url: "https://github.com/ylab-hi/octopusV"
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doi: "10.1093/bioinformatics/btaf599"
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licence:
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- "MIT"
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identifier: ""
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- txt:
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type: file
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description: OctopuSV stats text input
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pattern: "*.txt"
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ontologies:
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- edam: "http://edamontology.org/format_2330" # TXT
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output:
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sv_sizes_png:
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- - meta:
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type: map
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description: Sample information
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- ${prefix}_sv_sizes.png:
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type: file
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description: SV sizes plot (PNG)
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pattern: "*_sv_sizes.png"
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ontologies:
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- edam: "http://edamontology.org/format_3603" # PNG
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sv_sizes_svg:
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- - meta:
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type: map
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description: Sample information
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- ${prefix}_sv_sizes.svg:
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type: file
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description: SV sizes plot (SVG)
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pattern: "*_sv_sizes.svg"
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ontologies:
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- edam: "http://edamontology.org/format_3604" # SVG
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sv_types_png:
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- - meta:
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type: map
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description: Sample information
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- ${prefix}_sv_types.png:
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type: file
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description: SV types plot (PNG)
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pattern: "*_sv_types.png"
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ontologies:
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- edam: "http://edamontology.org/format_3603" # PNG
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sv_types_svg:
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- - meta:
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type: map
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description: Sample information
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- ${prefix}_sv_types.svg:
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type: file
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description: SV types plot (SVG)
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pattern: "*_sv_types.svg"
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ontologies:
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- edam: "http://edamontology.org/format_3604" # SVG
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chromosome_distribution_png:
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- - meta:
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type: map
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description: Sample information
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- ${prefix}_chromosome_distribution.png:
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type: file
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description: Chromosome distribution plot of structural variants (PNG)
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pattern: "*_chromosome_distribution.png"
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ontologies:
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- edam: "http://edamontology.org/format_3603" # PNG
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chromosome_distribution_svg:
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- - meta:
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type: map
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description: Sample information
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- ${prefix}_chromosome_distribution.svg:
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type: file
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description: Chromosome distribution plot of structural variants (SVG)
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pattern: "*_chromosome_distribution.svg"
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ontologies:
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- edam: "http://edamontology.org/format_3604" # SVG
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versions_octopusv:
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- - ${task.process}:
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type: string
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description: The name of the process
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- octopusv:
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type: string
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description: The name of the tool
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- python -c "import importlib.metadata as m; print(m.version('octopusv'))":
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type: eval
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description: The expression to obtain the version of the tool
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topics:
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versions:
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- - ${task.process}:
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type: string
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description: The name of the process
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- octopusv:
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type: string
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description: The name of the tool
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- python -c "import importlib.metadata as m; print(m.version('octopusv'))":
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type: eval
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description: The expression to obtain the version of the tool
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authors:
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- "@manascripts"
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maintainers:
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- "@manascripts"

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

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nextflow_process {
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name "Test Process OCTOPUSV_PLOT"
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script "../main.nf"
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process "OCTOPUSV_PLOT"
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tag "modules"
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tag "modules_nfcore"
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tag "octopusv"
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tag "octopusv/plot"
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test("homo_sapiens - stat - txt") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/octopusv/stat/stats_sk-n-as-severus-ont.txt', checkIfExists: true)
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]
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
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path(process.out.sv_sizes_png.get(0).get(1)),
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path(process.out.sv_types_png.get(0).get(1)),
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path(process.out.chromosome_distribution_png.get(0).get(1)),
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file(process.out.sv_sizes_svg.get(0).get(1)).name,
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file(process.out.sv_types_svg.get(0).get(1)).name,
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file(process.out.chromosome_distribution_svg.get(0).get(1)).name,
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process.out.findAll { key, val -> key.startsWith('versions') }
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).match() }
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)
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}
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}
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test("homo_sapiens - stat - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ],
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file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/octopusv/stat/stats_sk-n-as-severus-ont.txt', checkIfExists: true)
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]
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"""
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}
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}
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then {
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assert process.success
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assertAll(
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{ assert snapshot(sanitizeOutput(process.out)).match() }
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)
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}
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}
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}

‎modules/nf-core/octopusv/plot/tests/main.nf.test.snap‎

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{
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"homo_sapiens - stat - txt": {
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"content": [
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"test_sv_sizes.png:md5,a21190f74087066b2588f294fed9f242",
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"test_sv_types.png:md5,744cd764b0f54431922bb5047f252095",
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"test_chromosome_distribution.png:md5,8bff9ffb7cb75059b609616ceebb52a7",
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"test_sv_sizes.svg",
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"test_sv_types.svg",
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"test_chromosome_distribution.svg",
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{
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"versions_octopusv": [
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[
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"OCTOPUSV_PLOT",
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"octopusv",
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"0.3.3"
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]
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]
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}
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],
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"timestamp": "2026-05-22T14:14:00.146965966",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.10.4"
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}
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},
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"homo_sapiens - stat - stub": {
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"content": [
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{
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"chromosome_distribution_png": [
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[
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{
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"id": "test"
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},
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"test_chromosome_distribution.png:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"chromosome_distribution_svg": [
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[
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{
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"id": "test"
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},
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"test_chromosome_distribution.svg:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"sv_sizes_png": [
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[
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{
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"id": "test"
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},
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"test_sv_sizes.png:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"sv_sizes_svg": [
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[
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{
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"id": "test"
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},
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"test_sv_sizes.svg:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"sv_types_png": [
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[
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{
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"id": "test"
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},
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"test_sv_types.png:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"sv_types_svg": [
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[
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{
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"id": "test"
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},
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"test_sv_types.svg:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions_octopusv": [
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[
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"OCTOPUSV_PLOT",
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"octopusv",
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"0.3.3"
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]
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]
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}
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],
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"timestamp": "2026-05-22T14:14:07.088138028",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.10.4"
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}
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}
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}

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