Node degree distribution

[Schansiate]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/diseasemodulediscovery branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

[Copilot]

Pull request overview

This PR adds a node degree distribution summary for parsed input networks and integrates it into the final MultiQC report.

Changes:

• Extend graph_tool_parser.py / GRAPHTOOLPARSER to emit per-network node degree distribution YAML.
• Add a new MULTIQCFORMATTER module + multiqc_formatter.py to combine per-network distributions into a MultiQC custom-content YAML.
• Register the new MultiQC section and header config in assets/ and pipeline workflow wiring.

Reviewed changes

Copilot reviewed 6 out of 10 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
workflows/diseasemodulediscovery.nf	Wires the new node degree distribution output into MultiQC inputs via MULTIQCFORMATTER.
modules/local/multiqcformatter/main.nf	New process to generate MultiQC-ready YAML from distribution inputs + header.
modules/local/graphtoolparser/main.nf	Exposes node degree distribution YAML as an additional optional output.
conf/modules.config	Adds publishDir rules for MULTIQCFORMATTER.
bin/graph_tool_parser.py	Generates per-network node degree distribution YAML when parsing to gt.
bin/multiqc_formatter.py	New formatter script producing MultiQC custom-content YAML for the distribution plot.
assets/network_node_degree_distribution_header.yaml	New MultiQC custom-content header/template for node degree distribution.
assets/multiqc_config.yml	Adds the new section id to the custom_content ordering.
bin/network_annotation.py	Adds full-network and module-degree vertex properties to annotated subnetworks.
bin/visualize_modules.py	Adds runtime printing of pyvis version.

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[JohannesKersting]

@Schansiate
Please also update the output documentation and change to the new dependency container