Agentic Swarm Repo Cleanup
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components

Scaling tedious-but-necessary repository maintenance using AI agentic systems.

nf-core/modules contains hundreds of modules, many of which carry accumulated technical debt: missing stub blocks, inconsistent test coverage, outdated conventions, and absent documentation. These are the tasks that human developers rarely want to do — but they’re essential for the health of the ecosystem.

This project demonstrates how agentic AI swarms can systematically tackle this maintenance at scale, while keeping a human firmly in the loop for review and submission.

Track Record

Before the hackathon, this approach already delivered results:

48 modules identified as missing stub blocks (#4570)
40 modules stubbed and validated using automated AST analysis and nf-test snapshot verification
10 atomic PRs submitted (#11349–#11358), split by domain category for focused review
Every stub follows the canonical echo | gzip > convention (#5409)

Resources

The methodology, tooling, and lessons learned are documented in detail:

🌐 hvrinformatics.com — Engineering blog covering agentic bioinformatics development
📝 From Sandbox to Open Source: Deploying an Autonomous Swarm Against nf-core/modules — Deep dive into the stub generation pipeline
📝 From 1 PR to 10: How an AI Agent Split 40 Modules Into Atomic Pull Requests — How the agent decomposed a 40-module PR into reviewable units
🛠️ hvr-agentic-os — Open-source agentic swarm framework powering this project

Goal

Use agentic AI systems to identify and resolve systematic maintenance gaps across nf-core/modules — starting from the proven stub block foundation and expanding into additional cleanup workstreams during the hackathon.

Workstreams

1. Stub Block Completion (Proven)

Continue the #4570 initiative. Identify any remaining modules missing stubs, generate convention-compliant stub blocks, validate with nf-test, and submit atomic PRs.

2. Additional Cleanup Targets (Hackathon Scope)

Potential areas to tackle collaboratively during the event:

nf-test coverage gaps — Modules with incomplete or missing test snapshots
Topic channel migration — Updating modules to use modern Nextflow topic channels
Linting compliance — Resolving persistent nf-core modules lint warnings at scale
Documentation standardization — Ensuring consistent meta.yml and module documentation

The exact scope for workstreams 2+ will be refined at the hackathon based on community priorities and participant interest.

What Participants Will Do

Pick a workstream — Choose from stub completion, test coverage, topic migration, or linting cleanup.
Use the agentic workflow — or contribute manually, both are welcome.
Validate locally — Run nf-core modules lint and nf-test before submission.
Submit atomic PRs — One module or small batch per PR for focused review.

This project is suitable for all experience levels. Each task is self-contained and follows established nf-core contribution patterns.