# How to integrate Seqera MCP with Claude Code ```json { "title": "How to integrate Seqera MCP with Claude Code", "toolkit": "Seqera", "toolkit_slug": "seqera", "framework": "Claude Code", "framework_slug": "claude-code", "url": "https://composio.dev/toolkits/seqera/framework/claude-code", "markdown_url": "https://composio.dev/toolkits/seqera/framework/claude-code.md", "updated_at": "2026-05-12T10:25:32.226Z" } ``` ## Introduction Manage your Seqera directly from Claude Code with zero worries about OAuth hassles, API-breaking issues, or reliability and security concerns. You can do this in two different ways: - Via [Composio Connect](https://dashboard.composio.dev/login?utm_source=toolkits&utm_medium=framework_template&utm_campaign=claude-code&utm_content=composio_connect&next=%2F~%2Forg%2Fconnect%2Fclients%2Fclaude-code) - Direct and easiest approach - Via [Composio SDK](https://docs.composio.dev/docs?utm_source=toolkits&utm_medium=framework_template&utm_campaign=claude-code&utm_content=composio_sdk) - Programmatic approach with more control ## Also integrate Seqera with - [OpenAI Agents SDK](https://composio.dev/toolkits/seqera/framework/open-ai-agents-sdk) - [Claude Agent SDK](https://composio.dev/toolkits/seqera/framework/claude-agents-sdk) - [Claude Cowork](https://composio.dev/toolkits/seqera/framework/claude-cowork) - [Codex](https://composio.dev/toolkits/seqera/framework/codex) - [OpenClaw](https://composio.dev/toolkits/seqera/framework/openclaw) - [Hermes](https://composio.dev/toolkits/seqera/framework/hermes-agent) - [CLI](https://composio.dev/toolkits/seqera/framework/cli) - [Google ADK](https://composio.dev/toolkits/seqera/framework/google-adk) - [LangChain](https://composio.dev/toolkits/seqera/framework/langchain) - [Vercel AI SDK](https://composio.dev/toolkits/seqera/framework/ai-sdk) - [Mastra AI](https://composio.dev/toolkits/seqera/framework/mastra-ai) - [LlamaIndex](https://composio.dev/toolkits/seqera/framework/llama-index) - [CrewAI](https://composio.dev/toolkits/seqera/framework/crew-ai) ## TL;DR - Only one MCP URL to connect multiple apps with Claude Code with zero auth hassles. - Programmatic tool calling allows LLMs to write its code in a remote workbench to handle complex tool chaining. Reduces to-and-fro with LLMs for frequent tool calling. - Handling Large tool responses out of LLM context to minimize context rot. - Dynamic just-in-time access to 20,000 tools across 1000+ other Apps for cross-app workflows. It loads the tools you need, so LLMs aren't overwhelmed by tools you don't need. ## Connect Seqera to Claude Code ### Connecting Seqera to Claude Code using Composio 1. Add the Composio MCP to Claude ```bash claude mcp add --scope user --transport http composio https://connect.composio.dev/mcp ``` ## What is Claude Code? Claude Code is Anthropic's command line developer tool that lets you use Claude directly inside your terminal. Instead of switching between your editor, browser, and chat, you can stay in your project folder and ask Claude to help you build, debug, refactor, and understand code right where you're working. Key features include: - Terminal-Native Experience: Work with Claude directly in your command line without switching contexts - MCP Support: Built-in support for Model Context Protocol servers to extend Claude's capabilities - Project Context: Claude understands your project structure and can read, write, and modify files - Interactive Development: Ask questions, debug code, and get help in real-time while coding - Multi-Platform: Works on macOS, Linux, WSL, and Windows ## 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. ## Supported Tools | Tool slug | Name | Description | |---|---|---| | `SEQERA_CREATE_WAVE_CONTAINER` | Create Wave Container | Tool to submit a request to Wave for accessing a private container registry or building a container image on-the-fly. Use when you need to provision containers via Wave with Dockerfile, Conda recipe, or package specifications. Returns the name of the container made available by Wave. | | `SEQERA_GET_ORGANIZATION_DETAILS` | Get Organization Details | Tool to retrieve detailed information about a specific organization. | | `SEQERA_GET_SERVICE_INFO` | Get Service Info | Tool to retrieve information about the Seqera API service. Use when you need to check the service version and commit ID for troubleshooting. | | `SEQERA_GET_USER_INFO` | Get User Info | Tool to retrieve information about the authenticated user. Use when you need to fetch details of the current user after authentication. | | `SEQERA_GET_WAVE_BUILD_LOGS` | Get Wave Build Logs | Tool to get logs for a container build by build ID. Use when you need to troubleshoot or inspect the build process of a Wave container. | | `SEQERA_GET_WAVE_BUILD_STATUS` | Get Wave Build Status | Tool to retrieve the status of a Wave container build by build ID. Use when you need to check if a container build is completed and whether it succeeded. | | `SEQERA_INSPECT_WAVE_CONTAINER` | Inspect Wave Container | Tool to inspect container image metadata via Wave. Use when you need registry, manifest, digest, configuration, and OCI compatibility information about a container image. | | `SEQERA_LIST_ACTION_EVENT_TYPES` | List Action Event Types | Tool to list supported action event types. Use when you need to discover available triggers for pipelines, optionally filtered by workspace. | | `SEQERA_LIST_COMPUTE_ENVIRONMENTS` | List Compute Environments | Tool to retrieve a list of compute environments. Use when you need to page, sort, or filter compute environments accessible to your account. | | `SEQERA_LIST_ORGANIZATIONS` | List Organizations | Tool to list all organizations. Use after authentication to retrieve accessible Seqera organizations. | | `SEQERA_LIST_PIPELINES` | List Pipelines | Tool to list all pipelines accessible to the authenticated user. Use when you need to browse pipelines with optional pagination, sorting, or search filters. | | `SEQERA_LIST_WORKFLOWS` | List Workflows | Tool to list workflows. Use when you need to retrieve workflows filtered by workspace and paginated. | | `SEQERA_VALIDATE_ACTION_NAME` | Validate Action Name | Tool to validate action name. Use when you need to confirm if an action name is valid and available before creating an action. Returns validation status with details. | | `SEQERA_VALIDATE_PIPELINE_NAME` | Validate Pipeline Name | Tool to validate a pipeline name. Use when you need to check if a given pipeline name is valid and available before creating or updating one. | ## Supported Triggers None listed. ## Creating MCP Server - Stand-alone vs Composio SDK The Seqera MCP server is an implementation of the Model Context Protocol that connects Claude Code (and other AI assistants like Claude and Cursor) directly to your Seqera account. It provides structured and secure access so Claude can perform Seqera operations on your behalf. With Composio's managed implementation, you don't have to create your own developer app. For production, if you're building an end product, we recommend using your own credentials. The managed server helps you prototype fast and go from 0-1 faster. ## Step-by-step Guide ### 1. Prerequisites Before starting, make sure you have: - Claude Pro, Max, or API billing enabled Anthropic account - Composio API Key - A Seqera account - Basic knowledge of Python or TypeScript ### 1. Install Claude Code To install Claude Code, use one of the following methods based on your operating system: ```bash # macOS, Linux, WSL curl -fsSL https://claude.ai/install.sh | bash # Windows PowerShell irm https://claude.ai/install.ps1 | iex # Windows CMD curl -fsSL https://claude.ai/install.cmd -o install.cmd && install.cmd && del install.cmd ``` ### 2. Set up Claude Code Open a terminal, go to your project folder, and start Claude Code: - Claude Code will open in your terminal - Follow the prompts to sign in with your Anthropic account - Complete the authentication flow - Once authenticated, you can start using Claude Code ```bash cd your-project-folder claude ``` ### 3. Set up environment variables Create a .env file in your project root with the following variables: - COMPOSIO_API_KEY authenticates with Composio (get it from [Composio dashboard](https://dashboard.composio.dev/login?utm_source=toolkits&utm_medium=framework_template&utm_campaign=claude-code&utm_content=api_key&next=%2F~%2Forg%2Fconnect%2Fclients%2Fclaude-code)) - USER_ID identifies the user for session management (use any unique identifier) ```bash COMPOSIO_API_KEY=your_composio_api_key_here USER_ID=your_user_id_here ``` ### 4. Install Composio library No description provided. ```python pip install composio-core python-dotenv ``` ```typescript npm install @composio/core dotenv ``` ### 5. Generate Composio MCP URL No description provided. ```python import os from composio import Composio from dotenv import load_dotenv load_dotenv() COMPOSIO_API_KEY = os.getenv("COMPOSIO_API_KEY") USER_ID = os.getenv("USER_ID") composio_client = Composio(api_key=COMPOSIO_API_KEY) composio_session = composio_client.create( user_id=USER_ID, toolkits=["seqera"], ) COMPOSIO_MCP_URL = composio_session.mcp.url print(f"MCP URL: {COMPOSIO_MCP_URL}") print(f"\nUse this command to add to Claude Code:") print(f'claude mcp add --transport http seqera-composio "{COMPOSIO_MCP_URL}" --headers "X-API-Key:{COMPOSIO_API_KEY}"') ``` ```typescript import 'dotenv/config'; import { Composio } from '@composio/core'; const { COMPOSIO_API_KEY, USER_ID } = process.env; if (!COMPOSIO_API_KEY || !USER_ID) { throw new Error('COMPOSIO_API_KEY and USER_ID required in .env'); } const composioClient = new Composio({ apiKey: COMPOSIO_API_KEY }); const composioSession = await composioClient.create(USER_ID, { toolkits: ['seqera'], }); const composioMcpUrl = composioSession?.mcp.url; console.log(`MCP URL: ${composioMcpUrl}`); console.log(`\nUse this command to add to Claude Code:`); console.log(`claude mcp add --transport http seqera-composio "${composioMcpUrl}" --headers "X-API-Key:${COMPOSIO_API_KEY}"`); ``` ### 6. Run the script and copy the MCP URL No description provided. ```python python generate_mcp_url.py ``` ```typescript node --loader ts-node/esm generate_mcp_url.ts # or if using tsx tsx generate_mcp_url.ts ``` ### 7. Add Seqera MCP to Claude Code In your terminal, add the MCP server using the command from the previous step. The command format is: - claude mcp add registers a new MCP server with Claude Code - --transport http specifies that this is an HTTP-based MCP server - The server name (seqera-composio) is how you'll reference it - The URL points to your Composio Tool Router session - --headers includes your Composio API key for authentication After running the command, close the current Claude Code session and start a new one for the changes to take effect. ```bash claude mcp add --transport http seqera-composio "YOUR_MCP_URL_HERE" --headers "X-API-Key:YOUR_COMPOSIO_API_KEY" # Then restart Claude Code exit claude ``` ### 8. Verify the installation Check that your Seqera MCP server is properly configured. - This command lists all MCP servers registered with Claude Code - You should see your seqera-composio entry in the list - This confirms that Claude Code can now access Seqera tools If everything is wired up, you should see your seqera-composio entry listed: ```bash claude mcp list ``` ### 9. Authenticate Seqera The first time you try to use Seqera tools, you'll be prompted to authenticate. - Claude Code will detect that you need to authenticate with Seqera - It will show you an authentication link - Open the link in your browser (or copy/paste it) - Complete the Seqera authorization flow - Return to the terminal and start using Seqera through Claude Code Once authenticated, you can ask Claude Code to perform Seqera operations in natural language. For example: - "Launch a new Nextflow pipeline run" - "Monitor status of active pipeline jobs" - "List recent workflow execution logs" ## Complete Code ```python import os from composio import Composio from dotenv import load_dotenv load_dotenv() COMPOSIO_API_KEY = os.getenv("COMPOSIO_API_KEY") USER_ID = os.getenv("USER_ID") composio_client = Composio(api_key=COMPOSIO_API_KEY) composio_session = composio_client.create( user_id=USER_ID, toolkits=["seqera"], ) COMPOSIO_MCP_URL = composio_session.mcp.url print(f"MCP URL: {COMPOSIO_MCP_URL}") print(f"\nUse this command to add to Claude Code:") print(f'claude mcp add --transport http seqera-composio "{COMPOSIO_MCP_URL}" --headers "X-API-Key:{COMPOSIO_API_KEY}"') ``` ```typescript import 'dotenv/config'; import { Composio } from '@composio/core'; const { COMPOSIO_API_KEY, USER_ID } = process.env; if (!COMPOSIO_API_KEY || !USER_ID) { throw new Error('COMPOSIO_API_KEY and USER_ID required in .env'); } const composioClient = new Composio({ apiKey: COMPOSIO_API_KEY }); const composioSession = await composioClient.create(USER_ID, { toolkits: ['seqera'], }); const composioMcpUrl = composioSession?.mcp.url; console.log(`MCP URL: ${composioMcpUrl}`); console.log(`\nUse this command to add to Claude Code:`); console.log(`claude mcp add --transport http seqera-composio "${composioMcpUrl}" --headers "X-API-Key:${COMPOSIO_API_KEY}"`); ``` ## Conclusion You've successfully integrated Seqera with Claude Code using Composio's MCP server. Now you can interact with Seqera directly from your terminal using natural language commands. Key features of this setup: - Terminal-native experience without switching contexts - Natural language commands for Seqera operations - Secure authentication through Composio's managed MCP - Tool Router for dynamic tool discovery and execution Next steps: - Try asking Claude Code to perform various Seqera operations - Add more toolkits to your Tool Router session for multi-app workflows - Integrate this setup into your development workflow for increased productivity You can extend this by adding more toolkits, implementing custom workflows, or building automation scripts that leverage Claude Code's capabilities. ## How to build Seqera MCP Agent with another framework - [OpenAI Agents SDK](https://composio.dev/toolkits/seqera/framework/open-ai-agents-sdk) - [Claude Agent SDK](https://composio.dev/toolkits/seqera/framework/claude-agents-sdk) - [Claude Cowork](https://composio.dev/toolkits/seqera/framework/claude-cowork) - [Codex](https://composio.dev/toolkits/seqera/framework/codex) - [OpenClaw](https://composio.dev/toolkits/seqera/framework/openclaw) - [Hermes](https://composio.dev/toolkits/seqera/framework/hermes-agent) - [CLI](https://composio.dev/toolkits/seqera/framework/cli) - [Google ADK](https://composio.dev/toolkits/seqera/framework/google-adk) - [LangChain](https://composio.dev/toolkits/seqera/framework/langchain) - [Vercel AI SDK](https://composio.dev/toolkits/seqera/framework/ai-sdk) - [Mastra AI](https://composio.dev/toolkits/seqera/framework/mastra-ai) - [LlamaIndex](https://composio.dev/toolkits/seqera/framework/llama-index) - [CrewAI](https://composio.dev/toolkits/seqera/framework/crew-ai) ## Related Toolkits - [Excel](https://composio.dev/toolkits/excel) - Microsoft Excel is a robust spreadsheet application for organizing, analyzing, and visualizing data. It's the go-to tool for calculations, reporting, and flexible data management. - [21risk](https://composio.dev/toolkits/_21risk) - 21RISK is a web app built for easy checklist, audit, and compliance management. It streamlines risk processes so teams can focus on what matters. - [Abstract](https://composio.dev/toolkits/abstract) - Abstract provides a suite of APIs for automating data validation and enrichment tasks. It helps developers streamline workflows and ensure data quality with minimal effort. - [Addressfinder](https://composio.dev/toolkits/addressfinder) - Addressfinder is a data quality platform for verifying addresses, emails, and phone numbers. It helps you ensure accurate customer and contact data every time. - [Agenty](https://composio.dev/toolkits/agenty) - Agenty is a web scraping and automation platform for extracting data and automating browser tasks—no coding needed. It streamlines data collection, monitoring, and repetitive online actions. - [Ambee](https://composio.dev/toolkits/ambee) - Ambee is an environmental data platform providing real-time, hyperlocal APIs for air quality, weather, and pollen. Get precise environmental insights to power smarter decisions in your apps and workflows. - [Ambient weather](https://composio.dev/toolkits/ambient_weather) - Ambient Weather is a platform for personal weather stations with a robust API for accessing local, real-time, and historical weather data. Get detailed environmental insights directly from your own sensors for smarter apps and automations. - [Anonyflow](https://composio.dev/toolkits/anonyflow) - Anonyflow is a service for encryption-based data anonymization and secure data sharing. It helps organizations meet GDPR, CCPA, and HIPAA data privacy compliance requirements. - [Api ninjas](https://composio.dev/toolkits/api_ninjas) - Api ninjas offers 120+ public APIs spanning categories like weather, finance, sports, and more. Developers use it to supercharge apps with real-time data and actionable endpoints. - [Api sports](https://composio.dev/toolkits/api_sports) - Api sports is a comprehensive sports data platform covering 2,000+ competitions with live scores and 15+ years of stats. Instantly access up-to-date sports information for analysis, apps, or chatbots. - [Apify](https://composio.dev/toolkits/apify) - Apify is a cloud platform for building, deploying, and managing web scraping and automation tools called Actors. It lets you automate data extraction and workflow tasks at scale—no infrastructure headaches. - [Autom](https://composio.dev/toolkits/autom) - Autom is a lightning-fast search engine results data platform for Google, Bing, and Brave. Developers use it to access fresh, low-latency SERP data on demand. - [Beaconchain](https://composio.dev/toolkits/beaconchain) - Beaconchain is a real-time analytics platform for Ethereum 2.0's Beacon Chain. It provides detailed insights into validators, blocks, and overall network performance. - [Big data cloud](https://composio.dev/toolkits/big_data_cloud) - BigDataCloud provides APIs for geolocation, reverse geocoding, and address validation. Instantly access reliable location intelligence to enhance your applications and workflows. - [Bigpicture io](https://composio.dev/toolkits/bigpicture_io) - BigPicture.io offers APIs for accessing detailed company and profile data. Instantly enrich your applications with up-to-date insights on 20M+ businesses. - [Bitquery](https://composio.dev/toolkits/bitquery) - Bitquery is a blockchain data platform offering indexed, real-time, and historical data from 40+ blockchains via GraphQL APIs. Get unified, reliable access to complex on-chain data for analytics, trading, and research. - [Brightdata](https://composio.dev/toolkits/brightdata) - Brightdata is a leading web data platform offering advanced scraping, SERP APIs, and anti-bot tools. It lets you collect public web data at scale, bypassing blocks and friction. - [Builtwith](https://composio.dev/toolkits/builtwith) - BuiltWith is a web technology profiler that uncovers the technologies powering any website. Gain actionable insights into analytics, hosting, and content management stacks for smarter research and lead generation. - [Byteforms](https://composio.dev/toolkits/byteforms) - Byteforms is an all-in-one platform for creating forms, managing submissions, and integrating data. It streamlines workflows by centralizing form data collection and automation. - [Cabinpanda](https://composio.dev/toolkits/cabinpanda) - Cabinpanda is a data collection platform for building and managing online forms. It helps streamline how you gather, organize, and analyze responses. ## Frequently Asked Questions ### What are the differences in Tool Router MCP and Seqera MCP? 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. ### Can I use Tool Router MCP with Claude Code? Yes, you can. Claude Code 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. ### Can I manage the permissions and scopes for Seqera while using Tool Router? 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. ### How safe is my data with Composio Tool Router? 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. --- [See all toolkits](https://composio.dev/toolkits) · [Composio docs](https://docs.composio.dev/llms.txt)