Seqera MCP

Seqera MCP is a Model Context Protocol server that enables AI assistants to interact with the Seqera ecosystem. It provides access to Seqera Platform, Wave containers, nf-core modules, and bioinformatics data resources.

Features

• Seqera Platform integration: Launch, monitor, and manage Nextflow pipelines.
• Wave container service: Create containerized environments with conda/pip packages.
• nf-core modules: Search and execute 1000+ standardized bioinformatics modules.

Remote server

The hosted Seqera MCP server is available at:

https://mcp.seqera.io/mcp

Authentication

Seqera MCP supports two authentication methods:

• OAuth 2.1 (recommended): Interactive login through Seqera Platform. Your browser opens automatically to authenticate when connecting.
• Personal Access Token: Use your Seqera Platform access token as a Bearer token. Useful for clients that don't support OAuth.

Client setup

Claude Code

claude mcp add seqera --url https://mcp.seqera.io/mcp

Claude Desktop

1. Open Claude Desktop settings.
2. Select Add connectors.
3. Click Add custom connector.
4. Enter the URL: https://mcp.seqera.io/mcp.
5. Select OAuth as the authentication method.

Cursor

Create or edit ~/.cursor/mcp.json:

{
  "mcpServers": {
    "seqera": {
      "url": "https://mcp.seqera.io/mcp"
    }
  }
}

Restart Cursor to apply the configuration. On first use, your browser will open for authentication.

OpenAI Codex

First, enable the MCP client feature in ~/.codex/config.toml:

[features]
rmcp_client = true

Then add the Seqera MCP server and authenticate:

codex mcp add seqera --url https://mcp.seqera.io/mcp
codex mcp login seqera

VS Code

Create or edit ~/Library/Application Support/Code/User/mcp.json (macOS) or %APPDATA%\Code\User\mcp.json (Windows):

{
  "servers": {
    "seqera": {
      "url": "https://mcp.seqera.io/mcp",
      "type": "http"
    }
  }
}

Windsurf

Create or edit ~/.codeium/windsurf/mcp_config.json:

{
  "mcpServers": {
    "seqera": {
      "serverUrl": "https://mcp.seqera.io/mcp"
    }
  }
}

Using Personal Access Token

For clients that don't support OAuth, add your access token as a header:

{
  "mcpServers": {
    "seqera": {
      "url": "https://mcp.seqera.io/mcp",
      "headers": {
        "Authorization": "Bearer <YOUR_ACCESS_TOKEN>"
      }
    }
  }
}

Resources

• Model Context Protocol specification