diff --git a/platform-cloud/cloud-sidebar.json b/platform-cloud/cloud-sidebar.json index 018dcaaca..126a2a069 100644 --- a/platform-cloud/cloud-sidebar.json +++ b/platform-cloud/cloud-sidebar.json @@ -189,7 +189,8 @@ "seqerakit/templates" ] }, - "pipeline-actions/overview" + "pipeline-actions/overview", + "seqera-mcp" ] }, { diff --git a/platform-cloud/docs/seqera-mcp.md b/platform-cloud/docs/seqera-mcp.md new file mode 100644 index 000000000..b90f31241 --- /dev/null +++ b/platform-cloud/docs/seqera-mcp.md @@ -0,0 +1,127 @@ +--- +title: "Seqera MCP" +description: "Connect AI assistants to Seqera Platform using the Model Context Protocol" +date created: "2025-12-12" +tags: [mcp, integration, mcp-server, ai] +--- + +Seqera MCP is a [Model Context Protocol](https://modelcontextprotocol.io/) 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: + +```console +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](https://docs.seqera.io/platform-cloud/credentials/overview) as a Bearer token. Useful for clients that don't support OAuth. + +## Client setup + +### Claude Code + +```bash +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`: + +```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`: + +```toml +[features] +rmcp_client = true +``` + +Then add the Seqera MCP server and authenticate: + +```bash +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): + +```json +{ + "servers": { + "seqera": { + "url": "https://mcp.seqera.io/mcp", + "type": "http" + } + } +} +``` +### Windsurf + +Create or edit `~/.codeium/windsurf/mcp_config.json`: + +```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: + +```json +{ + "mcpServers": { + "seqera": { + "url": "https://mcp.seqera.io/mcp", + "headers": { + "Authorization": "Bearer " + } + } + } +} +``` + +## Resources + +- [Model Context Protocol specification](https://modelcontextprotocol.io/) +