Nextflow plugin for Claude and Codex

Build, migrate, test, debug and run Nextflow pipelines with Claude or Codex, connected to Nextflow Platform, Wave containers and nf-core.

The plugin bundles 28 skills and the hosted Seqera MCP server (https://mcp.seqera.io/mcp).

Install

In Claude Code:

/plugin marketplace add seqeralabs/nextflow-plugin
/plugin install nextflow@nextflow-plugin

Or from a shell:

claude plugin marketplace add seqeralabs/nextflow-plugin
claude plugin install nextflow@nextflow-plugin

Restart Claude Code after installing. The first time a Seqera tool is used, Claude Code opens the Nextflow Platform sign-in (OAuth). Skills that only work with local files and Nextflow do not need a Seqera account.

To make the plugin available to everyone working in a repository, add it to that repository's .claude/settings.json:

{
  "extraKnownMarketplaces": {
    "nextflow-plugin": {
      "source": { "source": "github", "repo": "seqeralabs/nextflow-plugin" }
    }
  },
  "enabledPlugins": { "nextflow@nextflow-plugin": true }
}

Codex

In the Codex app, open Plugins → Add → Add plugin marketplace, enter seqeralabs/nextflow-plugin as the source and install Nextflow. Or from a shell:

codex plugin marketplace add seqeralabs/nextflow-plugin
codex plugin add nextflow@nextflow-plugin

The same repository serves both hosts: Codex reads the Claude marketplace and plugin layout, and takes its listing (name, logo, starter prompts) from .codex-plugin/plugin.json.

Skills only

The skills follow the Agent Skills specification, so any skills-compatible agent (Claude Code, Codex, Cursor, OpenCode and others) can install them without the plugin. Use npx skills:

npx skills add seqeralabs/nextflow-plugin

Or the GitHub CLI (v2.90.0+):

gh skill install seqeralabs/nextflow-plugin

Both prompt for the skills and agents to install to. Update installed skills with npx skills update or gh skill update --all.

Installing skills this way does not configure the Seqera MCP server. For skills that use Nextflow Platform (e.g. launch-workflow), add https://mcp.seqera.io/mcp to your agent's MCP configuration.

What's included

Area	Skills
Build pipelines	build-nextflow-pipeline, nf-pipeline-design, nextflow-config, nextflow-schema, nextflow-output-patterns, search-existing-modules, run-module, create-container
Convert to Nextflow	build-nextflow-pipeline (Python, R and notebook playbooks), migrate-from-snakemake, audit-conversion-readiness, nextflow-schema (parameter triage), find-alternative-tools
Migrate and modernise	migrate-nextflow-code, nextflow-schema (schema migration), nf-plugin-development, nf-plugin-legacy-migration, maintain-nf-core-pipeline
Test and debug	nf-test (authoring and failure repair), repair-workflow (including static diagnostics), debug-local-run, debug-seqera-failed-run, nextflow-history (history, cache and narrative recaps), nf-data-lineage, nf-docker-scripts
Nextflow Platform	launch-workflow (with shared MCP connection reference), ce-credentials-setup, seqera-data-links, seqerakit
General	nextflow-development, install-nextflow

Licensing

Licensed under the Apache License, Version 2.0. Third-party attributions are in NOTICE, and per-file origin is recorded in sources.json.

The Apache-2.0 license covers the files in this repository. The hosted Seqera MCP server it connects to is a separate work, governed by its own license and Seqera's terms of service.