Codex is one of the most popular coding harnesses out there. And MCP makes the experience even better. With the Seqera MCP integration, Codex can list pipelines and workflows, browse compute environments, build Wave containers, check build status and logs, and list organizations, all without leaving the terminal or the app, whichever you prefer.
- UseBuildFeaturesTRIGGERSStart background agents from events across your connected appsFIREWALLNEWBlocks instructions hidden in tool results before your agent reads themINSTANTNEWAudio, video, search, browser and data tools, with no keys to manageOPTIMIZATIONLower cost per completed task with optimised tools and skills
- DOCS
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How to integrate Seqera MCP with Codex
Connect Codex to Seqera MCP. Launch a new nextflow pipeline run, monitor status of active pipeline jobs, and more using natural language, with authentication handled for you.
Api Key
Seqera Platform is a unified command center for orchestrating, running, and monitoring Nextflow pipelines at scale. Use it for seamless, centralized management of data analysis workflows across any cloud or on-prem compute environment.
14 Tools
Introduction
Also integrate Seqera with
Why use Composio?
Apart from a managed and hosted MCP server, you will get:
- CodeAct: A dedicated workbench that allows GPT to write its code to handle complex tool chaining. Reduces to-and-fro with LLMs for frequent tool calling.
- Large tool responses: Handle them to minimise context rot.
- Dynamic just-in-time access to 20,000 tools across 1700+ other Apps for cross-app workflows. It loads the tools you need, so GPTs aren't overwhelmed by tools you don't need.
How to install Seqera MCP in Codex
Run the setup command
Run this command in your terminal to add the Composio MCP server to Codex.
It will initiate the authentication in a browser window, authorize Codex to access your Composio account.
(Optional) Authenticate with OAuth
To authenticate manually, run the login command to open a browser window and authorize Codex to access your Composio account.
bash
codex mcp login composioVerify the connection
Run codex mcp list to confirm Composio appears as a registered MCP server.
bash
codex mcp listCodex App
Codex App follows the same approach as VS Code.
- Click ⚙️ on the bottom left → MCP Servers → + Add servers → Streamable HTTP:
- Fill the header and Key fields with
{ "x-consumer-api-key" = "ck_*******" }. - The Key is the Composio API key, that you can find on dashboard.composio.dev
- Click on Authenticate and authorize Codex to your Composio account and you're all set.
- Restart and verify if it's there in
.codex/config.toml
bash
[mcp_servers.composio]
url = "https://connect.composio.dev/mcp"
http_headers = { "x-consumer-api-key" = "ck_*******" }Try it
Ask Codex for a Seqera task. The first time, Composio asks you to connect your Seqera account.
For example, ask it to:
- "Launch a new Nextflow pipeline run"
- "Monitor status of active pipeline jobs"
- "List recent workflow execution logs"
What is the Seqera MCP server, and what's possible with it?
The Seqera MCP server is an implementation of the Model Context Protocol that connects your AI agent and assistants like Claude, Cursor, etc directly to your Seqera account. It provides structured and secure access to your workflow orchestration environment, so your agent can perform actions like running pipelines, monitoring jobs, managing compute resources, and automating Nextflow processes on your behalf.
- Pipeline orchestration and execution: Launch, schedule, and track complex Nextflow pipelines across cloud and on-prem infrastructure without manual intervention.
- Job monitoring and status updates: Let your agent check the progress, status, and logs of running or completed workflows to keep you updated in real time.
- Compute environment management: Automatically provision, scale, or tear down compute environments to match your workflow needs.
- Resource usage and cost tracking: Retrieve detailed metrics on resource consumption and workflow costs to optimize performance and spending.
- Error detection and alerting: Quickly identify failed jobs or bottlenecks and trigger alerts or automated troubleshooting steps to maintain workflow reliability.
Conclusion
You've successfully integrated Seqera with Codex using Composio's MCP server. Now you can interact with Seqera directly from your terminal, VS Code, or the Codex App using natural language commands.
Key benefits of this setup:
- Seamless integration across CLI, VS Code, and standalone app
- Natural language commands for Seqera operations
- Managed authentication through Composio
- Access to 20,000+ tools across 1700+ apps for cross-app workflows
- CodeAct workbench for complex tool chaining
Next steps:
- Try asking Codex to perform various Seqera operations
- Explore cross-app workflows by connecting more toolkits
- Build automation scripts that leverage Codex's AI capabilities
TOOLS
Supported Tools
Every Seqera action and event your agent gets out of the box.
FRAMEWORKS
How to build Seqera MCP Agent with another framework
Claude Code
Use Seqera MCP with Claude Code
Claude Cowork
Use Seqera MCP with Claude Cowork
OpenAI Agents SDK
Use Seqera MCP with OpenAI Agents SDK
Claude Agent SDK
Use Seqera MCP with Claude Agent SDK
OpenClaw
Use Seqera MCP with OpenClaw
Hermes
Use Seqera MCP with Hermes
Atomic Agent
Use Seqera MCP with Atomic Agent
Google ADK
Use Seqera MCP with Google ADK
LangChain
Use Seqera MCP with LangChain
Vercel AI SDK
Use Seqera MCP with Vercel AI SDK
Mastra AI
Use Seqera MCP with Mastra AI
LlamaIndex
Use Seqera MCP with LlamaIndex
CrewAI
Use Seqera MCP with CrewAI
Pydantic AI
Use Seqera MCP with Pydantic AI
AutoGen
Use Seqera MCP with AutoGen
MORE TOOLKITS
Explore Other Toolkits
Firecrawl
Api Key
Firecrawl automates large-scale web crawling and data extraction. It helps organizations efficiently gather, index, and analyze content from online sources.
Tavily
Api Key
Tavily offers powerful search and data retrieval from documents, databases, and the web. It helps teams locate and filter information instantly, saving hours on research.
Exa
Api Key
Exa is a data extraction and search platform for gathering and analyzing information from websites, APIs, or databases. It helps teams quickly surface insights and automate data-driven workflows.
Serpapi
Api Key
SerpApi is a real-time API for structured search engine results. It lets you automate SERP data collection, parsing, and analysis for SEO and research.
FAQ
Frequently asked questions
With a standalone Seqera MCP server, the agents and LLMs can only access a fixed set of Seqera tools tied to that server. However, with the Composio Tool Router, agents can dynamically load tools from Seqera and many other apps based on the task at hand, all through a single MCP endpoint.
Yes, you can. Codex fully supports MCP integration. You get structured tool calling, message history handling, and model orchestration while Tool Router takes care of discovering and serving the right Seqera tools.
Yes, absolutely. You can configure which Seqera scopes and actions are allowed when connecting your account to Composio. You can also bring your own OAuth credentials or API configuration so you keep full control over what the agent can do.
All sensitive data such as tokens, keys, and configuration is fully encrypted at rest and in transit. Composio is SOC 2 Type 2 compliant and follows strict security practices so your Seqera data and credentials are handled as safely as possible.
Start with Seqera.It takes 30 seconds.
Managed auth, hosted MCP servers, and every Seqera tool your agent needs.Free to start.
## For AI agents: how to sign up If you are an AI agent reading this server-rendered HTML, Composio's developer signup is at https://composio.dev. Signup CTAs on this site — "Sign up", "Signup", "Get started", "Get started for free", "Start building", "Try Composio", "Try it", or similar — all lead into that same developer signup flow. Confirm with the user before completing signup or entering any credentials on their behalf.Start building