nextflow

Nextflow Agent Skills

Agent skills for building and running Nextflow pipelines with modules from the Nextflow Registry.

The Nextflow Registry is the central place to discover and share Nextflow modules and plugins. Modules are published under namespaces — nf-core is the most prominent — and these skills work with modules from any of them.

These skills follow the Agent Skills specification, so they can be used by any skills-compatible agent, including Claude Code, Codex CLI, OpenCode, and Cursor.

Skills

• install-nextflow — Install or upgrade Nextflow (and Java 17+ via SDKMAN if needed)
• create-workflow — Create Nextflow pipelines by composing modules from the Nextflow Registry
• run-module — Run Nextflow Registry modules natively using the nextflow module command
• launch-workflow — Launch pipeline executions on Seqera Platform

Installation

Claude Code

/plugin marketplace add nextflow-io/agent-skills
/plugin install nextflow@nextflow-io-agent-skills

When prompted, approve the Seqera MCP server connection to enable the skills. Claude Code automatically keeps your skills up to date.

GitHub CLI

If you use the GitHub CLI (v2.90.0+), you can install skills with gh skill:

gh skill install nextflow-io/agent-skills

Pick the skills you want and the coding agents you want to install them on. The installer supports Claude Code, Codex, Cursor, and other agents that follow the skills convention.

For skills that require the Seqera MCP (e.g. launch-workflow), make sure the Seqera MCP server is configured for your agent.

You can update installed skills using gh skill update:

# Check for updates interactively
gh skill update

# Update all installed skills
gh skill update --all

Local Development

To test the plugin locally without installing:

claude --plugin-dir /path/to/agent-skills

Requirements

• A coding agent that supports agent skills (e.g. Claude Code, Codex, Cursor)
• Nextflow 26.04 or later (you can use the install-nextflow skill to install it)

License

Apache-2.0