Seqera MCP

Official hosted MCP server from Seqera Labs (the team behind Nextflow) that lets Claude launch and manage Nextflow pipelines, search nf-core modules, and pull public sequencing data — all from natural language.


Type	MCP server (hosted, HTTP)
Supplier	Seqera Labs
Availability	GA — endpoint live at `https://mcp.seqera.io/mcp`
Pricing	Free / OSS client access; a Seqera Platform account is required (Seqera has a free Cloud/Community tier; paid Pro/Enterprise tiers for larger compute)
Capabilities	Read/Write — launches and manages compute workflows on your Seqera account
Verified	works · 2026-07-20 — official docs confirm mcp.seqera.io/mcp endpoint (OAuth-gated)
Security	cleared · 2026-07-20 — provenance matches Seqera Labs official docs, hosted vendor service, write-capable

How to install

Claude Code — direct MCP add (HTTP transport; OAuth login opens in your browser on first connect):
```
claude mcp add --scope=user --transport=http seqera https://mcp.seqera.io/mcp
```
This is a hosted HTTP server — you do not run any local process. Claude Code connects to the remote endpoint directly. On first use a browser window opens for the Seqera OAuth 2.1 login.
Claude Desktop — Claude Desktop has no native remote-HTTP transport, so add it as a custom connector: Settings → Connectors → Add custom connector, enter URL https://mcp.seqera.io/mcp, and select OAuth as the authentication method. (If your Desktop build lacks the custom-connector UI, register a proxy stdio entry with mcp-remote instead: add to claude_desktop_config.json:
```
{
  "mcpServers": {
    "seqera": {
      "command": "npx",
      "args": ["-y", "mcp-remote", "https://mcp.seqera.io/mcp"]
    }
  }
}
```
)
Alternative auth (clients without OAuth) — use a Seqera Platform Personal Access Token as a Bearer token instead of the interactive OAuth flow. Generate the token in the Seqera Platform UI (Your tokens), then pass it via the --header flag:
```
claude mcp add --scope=user --transport=http seqera https://mcp.seqera.io/mcp --header "Authorization: Bearer <YOUR_SEQERA_TOKEN>"
```
(replace <YOUR_SEQERA_TOKEN> with the personal access token from your Seqera Platform account.)

What it does

Three tool groups:

Seqera Platform tools — launch, monitor, and manage Nextflow pipeline runs; create/inspect compute environments; provision containers via Wave.
nf-core tools — search the nf-core module library (1000+ standardized bioinformatics modules) and get analysis recommendations.
SRA tools — search and retrieve public sequencing data from NCBI SRA, EBI ENA, and GEO.

Primary use cases: Natural-language launching of nf-core pipelines (rnaseq, sarek, atacseq, etc.), managing Seqera compute environments, discovering public sequencing datasets to feed into a workflow.

Notes

Requires a Seqera Platform account. Because the server can launch compute workflows, treat it as a write-capable tool — pipeline runs may incur compute costs on your configured environment. Complements the nextflow-development skill (anthropics/life-sciences): that skill teaches Claude how to author and run nf-core pipelines locally, while this MCP drives runs and data retrieval through the hosted Seqera Platform.

The third-party Composio “Tool Router” integration exposes the same toolkit via a Composio-generated URL and an X-API-Key header; the official https://mcp.seqera.io/mcp endpoint above is the direct route and is preferred.

Sources

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