How to connect Seqera to Claude Cowork

Trusted by teams atAWSGleanZoomAirtable

30 min · no commitment · see it on your stack

Seqera logo
Claude Cowork logo
divider

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

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.

Claude Desktop connectors screen with Add custom connector selected

2. Add the Composio MCP server

Click Add custom connector and paste in the Composio MCP server URL:

bash
https://connect.composio.dev/mcp
Add custom connector dialog with Composio MCP server URL

3. Authorize in your browser

Click Connect. You'll be redirected to a browser window where you can authorize Composio to continue.

Composio authorization screen for Claude Cowork

4. Connect your Seqera account

Back in Cowork, ask the agent to connect to Seqera or give it any Seqera-related task.

For example, ask Cowork to:

  • "Launch a new Nextflow pipeline run"
  • "Monitor status of active pipeline jobs"
  • "List recent workflow execution logs"

It will prompt you to authenticate and authorize access.

That's it. Composio's tools are now available in Cowork, and your Seqera account is ready to use.

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 & Triggers

Tools
No tools available

How to build Seqera MCP Agent with another framework

FAQ

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.

Used by agents from

Context
Letta
glean
HubSpot
Agent.ai
Altera
DataStax
Entelligence
Rolai
Context
Letta
glean
HubSpot
Agent.ai
Altera
DataStax
Entelligence
Rolai
Context
Letta
glean
HubSpot
Agent.ai
Altera
DataStax
Entelligence
Rolai

Never worry about agent reliability

We handle tool reliability, observability, and security so you never have to second-guess an agent action.