jonasscheid/claude-nfcore-plugin
Plugin Claude Code
Comprehensive Claude Code plugin for nf-core Nextflow pipeline development. Includes skills for pipeline creation, module management, linting, testing, and release preparation following nf-core best practices.
jonasscheid/claude-nfcore-plugin
Agent
Autonomously 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.
jonasscheid/claude-nfcore-plugin
Agent
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.
jonasscheid/claude-nfcore-plugin
Agent
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.
jonasscheid/claude-nfcore-plugin
Agent
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.
jonasscheid/claude-nfcore-plugin
Agent
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.
jonasscheid/claude-nfcore-plugin
Agent
Creates nf-test tests for modules and workflows. Use when writing tests for new code, improving test coverage, creating snapshot tests, debugging test failures, or setting up testing infrastructure.
jonasscheid/claude-nfcore-plugin
Hook
Runs after a tool call finishes for Edit and Write tool calls, executing validate-nextflow-syntax.sh and format-nextflow-files.sh (2 commands). From jonasscheid/claude-nfcore-plugin.
jonasscheid/claude-nfcore-plugin
Hook
Runs before the agent uses a tool for Write tool calls, executing check-nf-core-conventions.sh. From jonasscheid/claude-nfcore-plugin.
jonasscheid/claude-nfcore-plugin
Skill Claude CodeCodex
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…
jonasscheid/claude-nfcore-plugin
Skill Claude CodeCodex
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.
jonasscheid/claude-nfcore-plugin
Skill Claude CodeCodex
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.
jonasscheid/claude-nfcore-plugin
Skill Claude CodeCodex
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).