# How to connect Seqera to Claude Cowork ```json { "title": "How to connect Seqera to Claude Cowork", "toolkit": "Seqera", "toolkit_slug": "seqera", "framework": "Claude Cowork", "framework_slug": "claude-cowork", "url": "https://composio.dev/toolkits/seqera/framework/claude-cowork", "markdown_url": "https://composio.dev/toolkits/seqera/framework/claude-cowork.md", "updated_at": "2026-05-12T10:25:32.226Z" } ``` ## Introduction Cowork is Anthropic's AI agent for knowledge work. Think of it as Claude Code for everything else. It works autonomously with your computer, local files, and applications to accomplish complex tasks. This guide walks you through the easiest and most secure way to connect your Seqera account to Cowork via Composio Connect, enabling it to launch a new Nextflow pipeline run, monitor status of active pipeline jobs, list recent workflow execution logs, and more such actions on your behalf without compromising your account security. ## 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) - [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) ## Connect Seqera to Claude Cowork ### Connecting Seqera to Claude Cowork 1. Open Customize In Claude Desktop, click Customize in the left sidebar, then select Connectors and click the + icon at the top. 2. Add the Composio MCP server Click Add custom connector and paste in the Composio MCP server URL: ```bash https://connect.composio.dev/mcp ``` ## What is Claude Cowork? Claude Cowork is Anthropic's agent for general knowledge work. It can use your computer, files, and connected applications to complete longer-running tasks across your work tools. With Composio Connect, Cowork can securely access apps like Seqera through MCP without you sharing account credentials directly with the agent. ## 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 connects Claude Cowork to your Seqera account through Composio. Once connected, Cowork can use the available Seqera tools and triggers to complete tasks on your behalf. ## Complete Code None listed. ## 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) - [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. 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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. ## 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 Cowork? Yes, you can. Claude Cowork 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)