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).
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-pluginRestart 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 }
}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-pluginThe 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.
| 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 (version, strict-syntax and boolean references), 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 |
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.