# How to integrate Seqera MCP with Mastra AI ```json { "title": "How to integrate Seqera MCP with Mastra AI", "toolkit": "Seqera", "toolkit_slug": "seqera", "framework": "Mastra AI", "framework_slug": "mastra-ai", "url": "https://composio.dev/toolkits/seqera/framework/mastra-ai", "markdown_url": "https://composio.dev/toolkits/seqera/framework/mastra-ai.md", "updated_at": "2026-05-12T10:25:32.226Z" } ``` ## Introduction This guide walks you through connecting Seqera to Mastra AI using the Composio tool router. By the end, you'll have a working Seqera agent that can launch a new nextflow pipeline run, monitor status of active pipeline jobs, list recent workflow execution logs through natural language commands. This guide will help you understand how to give your Mastra AI agent real control over a Seqera account through Composio's Seqera MCP server. Before we dive in, let's take a quick look at the key ideas and tools involved. ## 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 Code](https://composio.dev/toolkits/seqera/framework/claude-code) - [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) - [LlamaIndex](https://composio.dev/toolkits/seqera/framework/llama-index) - [CrewAI](https://composio.dev/toolkits/seqera/framework/crew-ai) ## TL;DR Here's what you'll learn: - Set up your environment so Mastra, OpenAI, and Composio work together - Create a Tool Router session in Composio that exposes Seqera tools - Connect Mastra's MCP client to the Composio generated MCP URL - Fetch Seqera tool definitions and attach them as a toolset - Build a Mastra agent that can reason, call tools, and return structured results - Run an interactive CLI where you can chat with your Seqera agent ## What is Mastra AI? Mastra AI is a TypeScript framework for building AI agents with tool support. It provides a clean API for creating agents that can use external services through MCP. Key features include: - MCP Client: Built-in support for Model Context Protocol servers - Toolsets: Organize tools into logical groups - Step Callbacks: Monitor and debug agent execution - OpenAI Integration: Works with OpenAI models via @ai-sdk/openai ## 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 your AI agent to Seqera. It provides structured and secure access so your agent can perform Seqera operations on your behalf through a secure, permission-based interface. 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: - Node.js 18 or higher - A Composio account with an active API key - An OpenAI API key - Basic familiarity with TypeScript ### 1. Getting API Keys for OpenAI and Composio OpenAI API Key - Go to the [OpenAI dashboard](https://platform.openai.com/settings/organization/api-keys) and create an API key. - You need credits or a connected billing setup to use the models. - Store the key somewhere safe. Composio API Key - Log in to the [Composio dashboard](https://dashboard.composio.dev?utm_source=toolkits&utm_medium=framework_docs). - Go to Settings and copy your API key. - This key lets your Mastra agent talk to Composio and reach Seqera through MCP. ### 2. Install dependencies Install the required packages. What's happening: - @composio/core is the Composio SDK for creating MCP sessions - @mastra/core provides the Agent class - @mastra/mcp is Mastra's MCP client - @ai-sdk/openai is the model wrapper for OpenAI - dotenv loads environment variables from .env ```bash npm install @composio/core @mastra/core @mastra/mcp @ai-sdk/openai dotenv ``` ### 3. Set up environment variables Create a .env file in your project root. What's happening: - COMPOSIO_API_KEY authenticates your requests to Composio - COMPOSIO_USER_ID tells Composio which user this session belongs to - OPENAI_API_KEY lets the Mastra agent call OpenAI models ```bash COMPOSIO_API_KEY=your_composio_api_key_here COMPOSIO_USER_ID=your_user_id_here OPENAI_API_KEY=your_openai_api_key_here ``` ### 4. Import libraries and validate environment What's happening: - dotenv/config auto loads your .env so process.env.* is available - openai gives you a Mastra compatible model wrapper - Agent is the Mastra agent that will call tools and produce answers - MCPClient connects Mastra to your Composio MCP server - Composio is used to create a Tool Router session ```typescript import "dotenv/config"; import { openai } from "@ai-sdk/openai"; import { Agent } from "@mastra/core/agent"; import { MCPClient } from "@mastra/mcp"; import { Composio } from "@composio/core"; import * as readline from "readline"; import type { AiMessageType } from "@mastra/core/agent"; const openaiAPIKey = process.env.OPENAI_API_KEY; const composioAPIKey = process.env.COMPOSIO_API_KEY; const composioUserID = process.env.COMPOSIO_USER_ID; if (!openaiAPIKey) throw new Error("OPENAI_API_KEY is not set"); if (!composioAPIKey) throw new Error("COMPOSIO_API_KEY is not set"); if (!composioUserID) throw new Error("COMPOSIO_USER_ID is not set"); const composio = new Composio({ apiKey: composioAPIKey as string, }); ``` ### 5. Create a Tool Router session for Seqera What's happening: - create spins up a short-lived MCP HTTP endpoint for this user - The toolkits array contains "seqera" for Seqera access - session.mcp.url is the MCP URL that Mastra's MCPClient will connect to ```typescript async function main() { const session = await composio.create( composioUserID as string, { toolkits: ["seqera"], }, ); const composioMCPUrl = session.mcp.url; console.log("Seqera MCP URL:", composioMCPUrl); ``` ### 6. Configure Mastra MCP client and fetch tools What's happening: - MCPClient takes an id for this client and a list of MCP servers - The headers property includes the x-api-key for authentication - getTools fetches the tool definitions exposed by the Seqera toolkit ```typescript const mcpClient = new MCPClient({ id: composioUserID as string, servers: { nasdaq: { url: new URL(composioMCPUrl), requestInit: { headers: session.mcp.headers, }, }, }, timeout: 30_000, }); console.log("Fetching MCP tools from Composio..."); const composioTools = await mcpClient.getTools(); console.log("Number of tools:", Object.keys(composioTools).length); ``` ### 7. Create the Mastra agent What's happening: - Agent is the core Mastra agent - name is just an identifier for logging and debugging - instructions guide the agent to use tools instead of only answering in natural language - model uses openai("gpt-5") to configure the underlying LLM ```typescript const agent = new Agent({ name: "seqera-mastra-agent", instructions: "You are an AI agent with Seqera tools via Composio.", model: "openai/gpt-5", }); ``` ### 8. Set up interactive chat interface What's happening: - messages keeps the full conversation history in Mastra's expected format - agent.generate runs the agent with conversation history and Seqera toolsets - maxSteps limits how many tool calls the agent can take in a single run - onStepFinish is a hook that prints intermediate steps for debugging ```typescript let messages: AiMessageType[] = []; console.log("Chat started! Type 'exit' or 'quit' to end.\n"); const rl = readline.createInterface({ input: process.stdin, output: process.stdout, prompt: "> ", }); rl.prompt(); rl.on("line", async (userInput: string) => { const trimmedInput = userInput.trim(); if (["exit", "quit", "bye"].includes(trimmedInput.toLowerCase())) { console.log("\nGoodbye!"); rl.close(); process.exit(0); } if (!trimmedInput) { rl.prompt(); return; } messages.push({ id: crypto.randomUUID(), role: "user", content: trimmedInput, }); console.log("\nAgent is thinking...\n"); try { const response = await agent.generate(messages, { toolsets: { seqera: composioTools, }, maxSteps: 8, }); const { text } = response; if (text && text.trim().length > 0) { console.log(`Agent: ${text}\n`); messages.push({ id: crypto.randomUUID(), role: "assistant", content: text, }); } } catch (error) { console.error("\nError:", error); } rl.prompt(); }); rl.on("close", async () => { console.log("\nSession ended."); await mcpClient.disconnect(); process.exit(0); }); } main().catch((err) => { console.error("Fatal error:", err); process.exit(1); }); ``` ## Complete Code ```typescript import "dotenv/config"; import { openai } from "@ai-sdk/openai"; import { Agent } from "@mastra/core/agent"; import { MCPClient } from "@mastra/mcp"; import { Composio } from "@composio/core"; import * as readline from "readline"; import type { AiMessageType } from "@mastra/core/agent"; const openaiAPIKey = process.env.OPENAI_API_KEY; const composioAPIKey = process.env.COMPOSIO_API_KEY; const composioUserID = process.env.COMPOSIO_USER_ID; if (!openaiAPIKey) throw new Error("OPENAI_API_KEY is not set"); if (!composioAPIKey) throw new Error("COMPOSIO_API_KEY is not set"); if (!composioUserID) throw new Error("COMPOSIO_USER_ID is not set"); const composio = new Composio({ apiKey: composioAPIKey as string }); async function main() { const session = await composio.create(composioUserID as string, { toolkits: ["seqera"], }); const composioMCPUrl = session.mcp.url; const mcpClient = new MCPClient({ id: composioUserID as string, servers: { seqera: { url: new URL(composioMCPUrl), requestInit: { headers: session.mcp.headers, }, }, }, timeout: 30_000, }); const composioTools = await mcpClient.getTools(); const agent = new Agent({ name: "seqera-mastra-agent", instructions: "You are an AI agent with Seqera tools via Composio.", model: "openai/gpt-5", }); let messages: AiMessageType[] = []; const rl = readline.createInterface({ input: process.stdin, output: process.stdout, prompt: "> ", }); rl.prompt(); rl.on("line", async (input: string) => { const trimmed = input.trim(); if (["exit", "quit"].includes(trimmed.toLowerCase())) { rl.close(); return; } messages.push({ id: crypto.randomUUID(), role: "user", content: trimmed }); const { text } = await agent.generate(messages, { toolsets: { seqera: composioTools }, maxSteps: 8, }); if (text) { console.log(`Agent: ${text}\n`); messages.push({ id: crypto.randomUUID(), role: "assistant", content: text }); } rl.prompt(); }); rl.on("close", async () => { await mcpClient.disconnect(); process.exit(0); }); } main(); ``` ## Conclusion You've built a Mastra AI agent that can interact with Seqera through Composio's Tool Router. You can extend this further by: - Adding other toolkits like Gmail, Slack, or GitHub - Building a web-based chat interface around this agent - Using multiple MCP endpoints to enable cross-app workflows ## 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 Code](https://composio.dev/toolkits/seqera/framework/claude-code) - [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) - [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 Mastra AI? Yes, you can. Mastra AI 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)