# How to integrate Seqera MCP with Atomic Agent ```json { "title": "How to integrate Seqera MCP with Atomic Agent", "toolkit": "Seqera", "toolkit_slug": "seqera", "framework": "Atomic Agent", "framework_slug": "atomic-agent", "url": "https://composio.dev/toolkits/seqera/framework/atomic-agent", "markdown_url": "https://composio.dev/toolkits/seqera/framework/atomic-agent.md", "updated_at": "2026-08-11T13:14:34.898Z" } ``` ## Introduction Atomic Agent is an open-source AI agent that runs on your machine and supports local models through llama.cpp. Connect it to 1,500+ apps through Composio, including Seqera. This guide uses Atomic Agent's built-in Composio integration. You need Atomic Agent v0.5.6 or later, your own Composio API key, and a Seqera account. See the [Atomic Agent documentation](https://atomicagent.io/docs/?cta_placement=atomic-agent-docs) for installation instructions. ## 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) - [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) - [Pydantic AI](https://composio.dev/toolkits/seqera/framework/pydantic-ai) - [AutoGen](https://composio.dev/toolkits/seqera/framework/autogen) ## TL;DR ### How Atomic Agent connects to Seqera Atomic Agent connects to Composio's Tool Router over Streamable HTTP MCP. It discovers the tools needed for your request, and Composio handles account authentication. Execution and account-connection tools follow Atomic Agent's configured approval policy. Review any approval prompt before allowing an action on your connected account. ## Connect Seqera to Atomic Agent ### Connect Seqera to Atomic Agent - Sign up or sign in to the [Composio dashboard](https://dashboard.composio.dev/?cta_placement=atomic-agent-api-key). Copy your API key. - In Atomic Agent, open the Integrations tab and select Composio. Select API key, press e, paste the key, and press Enter. The tools become available immediately, without a restart. - Ask Atomic Agent to do something in Seqera. It searches Composio for the right tool. - On first use, open the sign-in link returned in the chat. Connect your Seqera account, then return to Atomic Agent to continue. ### Headless setup Add the following line to ~/.atomic-agent/.env, replacing YOUR_COMPOSIO_API_KEY with your key. Start Atomic Agent after saving the file. ```bash COMPOSIO_API_KEY=YOUR_COMPOSIO_API_KEY ``` ## 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. ## Troubleshooting ### Why is my API key rejected? Copy the key directly from the Composio dashboard. Atomic Agent requires ASCII characters because it sends the key in an HTTP header. Remove any extra characters introduced when copying. ### Why are Composio tools unavailable after saving a key? Check that you use Atomic Agent v0.5.6 or later and that Composio is enabled in your configuration. A "composio": { "enabled": false } setting disables the integration while keeping the saved key on disk. ### Does Composio have a free plan? The Hobby plan includes 100,000 tool calls per month. Composio-managed OAuth apps have a lower included allowance. See [Composio pricing](/pricing) for the current limits that apply to your connection. ## Complete Code None listed. ## Conclusion ### Use Seqera from Atomic Agent With your account connected, ask Atomic Agent to work with Seqera in natural language. You can connect more apps through the same Composio integration as you need them. Visit the [Atomic Agent website](https://atomicagent.io/?cta_placement=atomic-agent-site) or inspect the [Atomic Agent source code](https://github.com/AtomicBot-ai/atomic-agent?cta_placement=atomic-agent-repo). ## 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) - [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) - [Pydantic AI](https://composio.dev/toolkits/seqera/framework/pydantic-ai) - [AutoGen](https://composio.dev/toolkits/seqera/framework/autogen) ## 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. - [AccuWeather](https://composio.dev/toolkits/accu_weather) - AccuWeather is a global weather service providing current conditions, forecasts, MinuteCast precipitation, alerts, and lightning data. Use it for fast, localized forecasts and real-time weather alerts. - [Adafruit IO](https://composio.dev/toolkits/adafruit_io) - Adafruit IO is Adafruit's cloud platform for connected device and IoT project data. It helps you store, visualize, and act on sensor feeds without running your own backend. - [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. - [Agentql](https://composio.dev/toolkits/agentql) - Agentql is a toolkit that connects AI agents to the web using a specialized query language. It enables structured web interaction and data extraction for smarter automations. - [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. - [ApexVerify](https://composio.dev/toolkits/apexverify) - ApexVerify is a contact-data validation service for emails and phone numbers. Use it to normalize, verify, and clean leads before they enter your systems. - [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. - [Beach Day API](https://composio.dev/toolkits/beach_day_api) - Beach Day API is a beach intelligence service for search, conditions, scores, rules, amenities, tides, and country coverage. Use it to power trip planning, surf reports, safety checks, and location-aware beach discovery. - [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. ## 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 Atomic Agent? Yes, you can. Atomic Agent 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)