Help us improve
Share bugs, ideas, or general feedback.
Share bugs, ideas, or general feedback.
Share bugs, ideas, or general feedback.
By jonasscheid
Develop and maintain nf-core Nextflow pipelines with automated module creation, linting, testing, and release preparation. Enforces nf-core conventions and strict syntax rules, with autonomous agents that fix lint errors, review code, create tests, and generate migration plans.
npx claudepluginhub jonasscheid/claude-nfcore-pluginAutonomously fixes nf-core lint errors and warnings. Use when there are lint issues to fix, after running lint, when preparing for release, or when the pipeline has validation errors.
Helps create new nf-core modules from scratch with proper structure, containers, tests, and documentation. Use when wrapping new bioinformatics tools, creating custom modules, or contributing modules to nf-core/modules.
Reviews code for nf-core compliance and best practices. Use proactively when reviewing PRs, checking code quality, ensuring nf-core standards are met, or validating pipeline changes before merge.
Analyzes existing pipelines and plans architectural changes, migrations, and refactoring. Use when modernizing a pipeline, migrating to strict syntax, restructuring workflows, or planning architectural changes.
Explores and analyzes nf-core pipeline structure, understanding workflows, modules, and configurations. Use proactively when needing to understand a pipeline's architecture, trace data flow, find specific processes, or when the user asks how a pipeline works.
This skill should be used when the user asks about "nf-core conventions", "strict syntax", "naming conventions", "output patterns", "coding style", "best practices", "parameter naming", "channel naming", "process labels", or how to structure nf-core code correctly. Covers strict syntax rules (Q2 2026 deadline), output glob patterns, and naming conventions.
This skill should be used when the user asks to "create a module", "install module", "update module", "patch module", "lint module", "create subworkflow", "install subworkflow", "update subworkflow", or any `nf-core modules` or `nf-core subworkflows` operation.
This skill should be used when the user asks to "run tests", "write nf-test", "create test cases", "debug test failures", "update snapshots", "validate pipeline outputs", "run nf-test", or mentions nf-test, snapshot testing, stub runs, or pipeline-level testing.
This skill should be used when the user asks to "create pipeline", "lint pipeline", "build schema", "sync template", "release pipeline", "validate params", or any `nf-core pipelines` operation. Covers the full nf-core pipeline lifecycle including Nextflow strict syntax validation (Q2 2026 deadline).
Modifies files
Hook triggers on file write and edit operations
Uses power tools
Uses Bash, Write, or Edit tools
Share bugs, ideas, or general feedback.
Own this plugin?
Verify ownership to unlock analytics, metadata editing, and a verified badge.
Sign in to claimOwn this plugin?
Verify ownership to unlock analytics, metadata editing, and a verified badge.
Sign in to claimBased on adoption, maintenance, documentation, and repository signals. Not a security audit or endorsement.
Jarvis-CD MCP - Pipeline Management for High-Performance Computing with comprehensive workflow operations
20 ENCODE API tools + 47 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.
Self-documenting, self-improving framework for analytical repositories
Design complex n8n workflows with AI assistance - loops, branching, error handling
Complete Azure Data Factory expertise for pipeline JSON development, validation, and optimization (2025-2026). This plugin should be used for ADF pipeline creation, activity configuration, linked services, datasets, triggers, expressions, CI/CD, Microsoft Fabric integration, Databricks orchestration, ML pipeline patterns, and debugging.
Access ClinicalTrials.gov data. The Clinical Trials Connector gives Claude access to ClinicalTrials.gov, the NIH/NLM registry of FDA-regulated clinical studies conducted worldwide.
A Claude Code plugin for nf-core Nextflow pipeline development. Skills mirror the nf-core CLI structure for intuitive use. Agents handle autonomous tasks like lint fixing, module creation, and code review.
| Skill | Description | Maps to CLI |
|---|---|---|
pipelines | Create, lint, schema, sync, and release pipelines | nf-core pipelines <action> |
modules | Create, install, update, patch, and lint modules/subworkflows | nf-core modules/subworkflows <action> |
nf-test | Run and manage nf-test tests | nf-test |
best-practices | Quick reference for nf-core conventions | — |
| Agent | Description |
|---|---|
pipeline-explorer | Explore and analyze pipeline structure (read-only) |
pipeline-architect | Plan pipeline migrations and refactoring |
lint-fixer | Autonomously fix lint errors |
nf-core-reviewer | Review code for nf-core compliance |
test-writer | Create nf-test tests |
module-creator | Create new modules from scratch |
.nf and .config filesgit clone https://github.com/jonasscheid/claude-nfcore-plugin.git
claude --plugin-dir ./claude-nfcore-plugin
To avoid passing --plugin-dir every time:
alias claude='claude --plugin-dir /absolute/path/to/claude-nfcore-plugin'
Once installed, use skills with the /nf-core: prefix:
/nf-core:pipelines lint # Lint your pipeline
/nf-core:pipelines create # Create a new pipeline
/nf-core:modules install fastqc # Install a module
/nf-core:modules create bwa/mem # Create a new module
/nf-core:nf-test # Run tests
/nf-core:best-practices # View conventions reference
Conda/Mamba (Recommended)
mamba create -n nf-core nf-core nf-test nextflow -c conda-forge -c bioconda
pip
pip install nf-core
# nf-test and Nextflow must be installed separately:
# nf-test: curl -fsSL https://get.nf-test.com | bash
# Nextflow: curl -s https://get.nextflow.io | bash
uv
uv pip install nf-core
# nf-test and Nextflow must be installed separately
On first skill invocation, you'll be asked which package manager you use. Your preference is stored in nf-core.local.md within the plugin directory and used for all subsequent commands.
.nf and .config files via hooksChannel., implicit closures, shell:)channel. instead of Channel.snake_caseskip_X not run_X)path("${prefix}.ext") not path("*.ext"))dev branch for nf-core repos.
├── .claude-plugin/
│ └── plugin.json # Plugin manifest
├── agents/ # 6 autonomous agents
├── hooks/
│ └── hooks.json # Validation hooks
├── scripts/ # Hook scripts
├── shared/ # Reference docs read by skills and agents
│ ├── conventions.md # nf-core conventions, strict syntax, naming
│ ├── module-template.md # Module structure and templates
│ └── test-patterns.md # nf-test patterns and assertions
└── skills/ # 4 user-invocable skills
├── best-practices/
├── modules/
├── nf-test/
└── pipelines/
MIT