seqeralabs · christopher-hakkaart · Dec 9, 2025 · Dec 10, 2025
diff --git a/.gitmodules b/.gitmodules
diff --git a/docusaurus.config.js b/docusaurus.config.js
@@ -148,6 +148,24 @@ export default async function createConfigAsync() {
     },
   ];
 
+  const docs_mcp = [
+    "@docusaurus/plugin-content-docs",
+    {
+      id: "mcp",
+      routeBasePath: "/mcp",
+      path: "mcp_docs",
+      remarkPlugins: [
+        (await import("remark-code-import")).default,
+        (await require("remark-math")).default,
+        (await import("docusaurus-remark-plugin-tab-blocks")).default,
+        (await require("remark-yaml-to-table")).default,
+      ],
+      rehypePlugins: [(await require("rehype-katex")).default],
+      editUrl: "https://github.com/seqeralabs/docs/tree/master/",
+      sidebarPath: "./mcp_docs/sidebar.json",
+    },
+  ];
+
   console.log(
     "\n  EXCLUDE_CHANGELOG: " + (process.env.EXCLUDE_CHANGELOG ? true : false),
     "\n  EXCLUDE_PLATFORM_ENTERPRISE: " +
@@ -161,6 +179,7 @@ export default async function createConfigAsync() {
     "\n  EXCLUDE_MULTIQC: " + (process.env.EXCLUDE_MULTIQC ? true : false),
     "\n  EXCLUDE_FUSION: " + (process.env.EXCLUDE_FUSION ? true : false),
     "\n  EXCLUDE_WAVE: " + (process.env.EXCLUDE_WAVE ? true : false),
+    "\n  EXCLUDE_MCP: " + (process.env.EXCLUDE_MCP ? true : false),
     "\n  INCLUDE_NEXT: " + (process.env.INCLUDE_NEXT ? true : false),
   );
 
@@ -265,6 +284,7 @@ export default async function createConfigAsync() {
       process.env.EXCLUDE_MULTIQC ? null : docs_multiqc,
       process.env.EXCLUDE_FUSION ? null : docs_fusion,
       process.env.EXCLUDE_WAVE ? null : docs_wave,
+      process.env.EXCLUDE_MCP ? null : docs_mcp,
 
       // Disable expensive bundler options.
       // https://github.com/facebook/docusaurus/pull/11176
@@ -367,6 +387,11 @@ export default async function createConfigAsync() {
             label: "Fusion",
             position: "left",
           },
+          {
+            to: "/mcp",
+            label: "MCP",
+            position: "left",
+          },
           {
             to: "https://training.nextflow.io/latest/",
             html: 'Nextflow Training <svg width="12" height="12" aria-hidden="true" viewBox="0 0 24 24" class="iconExternalLink_nPIU" style="margin-left:6px;opacity:0.6;"><path fill="currentColor" d="M21 13v10h-21v-19h12v2h-10v15h17v-8h2zm3-12h-10.988l4.035 4-6.977 7.07 2.828 2.828 6.977-7.07 4.125 4.172v-11z"></path></svg>',

diff --git a/mcp_docs/index.md b/mcp_docs/index.md
@@ -0,0 +1,129 @@
+---
+title: Seqera MCP
+description: "Connect AI assistants to Seqera Platform using the Model Context Protocol"
+date: "09 Dec 2024"
+tags: [mcp, ai, integration]
+---
+
+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
+- **Data resources**: Access reference genomes, sequencing data, and scientific literature
+
+## 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
+
+### 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.
+
+### 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"
+    }
+  }
+}
+```
+
+### 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
+
+### 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
+```
+
+### 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 <YOUR_ACCESS_TOKEN>"
+      }
+    }
+  }
+}
+```
+
+## Resources
+
+- [Model Context Protocol specification](https://modelcontextprotocol.io/)
+- [Seqera MCP repository](https://github.com/seqeralabs/seqera-mcp)
diff --git a/mcp_docs/sidebar.json b/mcp_docs/sidebar.json
@@ -0,0 +1,5 @@
+{
+  "sidebar": [
+    "index"
+  ]
+}
diff --git a/src/theme/DocSidebar/Desktop/ProductSwitcher/index.jsx b/src/theme/DocSidebar/Desktop/ProductSwitcher/index.jsx
@@ -25,6 +25,7 @@ const products = [
   { name: "MultiQC", url: "/multiqc" },
   { name: "Wave", url: "/wave" },
   { name: "Fusion", url: "/fusion" },
+  { name: "MCP", url: "/mcp" },
 ];
 
 const ProductSwitcher = ({ isDropdown }) => {

diff --git a/src/theme/Navbar/Layout/SeqeraHeader/HeaderDesktop/NavItems/index.jsx b/src/theme/Navbar/Layout/SeqeraHeader/HeaderDesktop/NavItems/index.jsx
@@ -86,7 +86,12 @@ const NavItems = ({ isDark = false, hideMenu }) => {
                 Fusion
               </ActiveLink>
             </li>
-             </ul>
+            <li>
+            <ActiveLink url="/mcp" customClasses={styles.navItemSpacing}>
+                MCP
+              </ActiveLink>
+            </li>
+            </ul>
         <ul className={styles.navList} style={{marginRight: '0.5rem'}}>
           <li>
             <a className={styles.linkContainer} href="https://training.nextflow.io/latest/">