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How to connect Seqera to Claude

Connect Claude Web, Desktop and Cowork to Seqera MCP. Launch a new nextflow pipeline run, monitor status of active pipeline jobs, and more using natural language, with authentication handled for you.

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Seqera Platform is a unified command center for orchestrating, running, and monitoring Nextflow pipelines at scale. Use it for seamless, centralized management of data analysis workflows across any cloud or on-prem compute environment.

14 Tools

Introduction

Claude is Anthropic's AI assistant, available on the web, in the desktop app, and on mobile. Cowork is its agent for knowledge work, and it runs on all of those surfaces too. Connected to your apps, Claude can work with your files and services to accomplish complex tasks on your behalf.

This guide walks you through the easiest and most secure way to connect your Seqera account to Claude 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.

Setup is the same on Claude Web, Desktop, and Cowork, and you only need to do it once. The connector is tied to your account, so it's available in all three.

Also integrate Seqera with

OpenAI Agents SDKClaude Agent SDKClaude CodeCodexOpenClawHermesAtomic AgentGoogle ADKLangChainVercel AI SDKMastra AILlamaIndexCrewAIPydantic AIAutoGen

Connecting Seqera to Claude Web, Desktop, and Cowork

Two ways to add the Composio connector. Pick whichever you prefer.

1. Add with one click

Click the button. Claude opens with the Composio connector filled in. Click Add, then go to step 2.

Add to Claude

Add manually

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

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

2. 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 Web, Desktop, and Cowork

3. Connect your Seqera account

Back in Claude, ask it to connect to Seqera or give it any Seqera-related task.

For example, ask Claude 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 Claude, and your Seqera account is ready to use.

What is the Seqera Claude Connector, 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.

Troubleshooting

1. Why does Claude not use the Composio connector for Seqera?

The connector can show as connected, but Claude must use it in each Seqera conversation.

  • Click + at the lower left of the chat, or type /.
  • Hover Connectors.
  • Turn on Composio.
  • Ask Claude to connect to Seqera again.

2. Why does Claude show an MCP server error before Seqera connects?

Claude can show Couldn't reach the MCP server or Authorization with the MCP server failed when you add the connector for Seqera.

  • Check that the connector URL is https://connect.composio.dev/mcp.
  • Connectors run from Anthropic's cloud, so your device network is usually not the problem.
  • Add the connector again from Customize > Connectors, then ask Claude to connect Seqera.
  • If it fails again, send the error and the ofid_ reference id to support@composio.dev.

3. Why does the Seqera authorization link not work?

The Composio connector is one server. Your Seqera account connects separately when Claude asks for it.

  • If the browser does not open, or the link expires, ask Claude to retry the Seqera connection.
  • Composio creates a fresh Seqera authorization link.
  • Open that link in your browser and finish the Seqera sign-in.

4. Why do Seqera actions fail after they worked before?

The Seqera connection can expire or lose permission.

  • Ask Claude to inspect the Seqera connection.
  • If the connection is unhealthy, disconnect it when Claude prompts you.
  • Reconnect the Seqera account and retry the action.
  • If Claude shows a permission prompt, approve it before Claude changes data in Seqera.
  • If the action still fails with a permission error, check that the connected account has that permission in Seqera itself.

5. How do I switch to a different Seqera account?

Claude can manage the Seqera connection for you.

  • Ask Claude to disconnect or delete the current Seqera account.
  • Ask Claude to connect Seqera again.
  • Open the new Composio authorization link for Seqera.
  • Sign in with the other Seqera account in the browser.
  • After the account connects, ask Claude to retry the Seqera task.

6. Why is my Seqera connection missing in Claude Desktop or on a Team plan?

The connector belongs to your Claude account, so your Seqera connection works in Claude Web, Desktop, and Cowork.

  • In Claude Desktop, open Customize > Connectors.
  • Next to Composio, click ⋮ and click Clear cache.
  • If Seqera tools still do not appear, click ⋮, disconnect, remove the connector, and add it again.
  • On Team or Enterprise, an Owner or Primary Owner must enable the connector before you can connect Seqera.
TOOLS

Supported Tools

Every Seqera action and event your agent gets out of the box.

Create Wave Container

Tool to submit a request to Wave for accessing a private container registry or building a container image on-the-fly.

Get Organization Details

Tool to retrieve detailed information about a specific organization.

Get Service Info

Tool to retrieve information about the Seqera API service.

Get User Info

Tool to retrieve information about the authenticated user.

Get Wave Build Logs

Tool to get logs for a container build by build ID.

Get Wave Build Status

Tool to retrieve the status of a Wave container build by build ID.

Inspect Wave Container

Tool to inspect container image metadata via Wave.

List Action Event Types

Tool to list supported action event types.

List Compute Environments

Tool to retrieve a list of compute environments.

List Organizations

Tool to list all organizations.

List Pipelines

Tool to list all pipelines accessible to the authenticated user.

List Workflows

Tool to list workflows.

Validate Action Name

Tool to validate action name.

Validate Pipeline Name

Tool to validate a pipeline name.

FRAMEWORKS

How to build Seqera MCP Agent with another framework

OpenAI Agents SDK logo

OpenAI Agents SDK

Use Seqera MCP with OpenAI Agents SDK

Claude Agent SDK logo

Claude Agent SDK

Use Seqera MCP with Claude Agent SDK

Claude Code logo

Claude Code

Use Seqera MCP with Claude Code

Codex logo

Codex

Use Seqera MCP with Codex

OpenClaw logo

OpenClaw

Use Seqera MCP with OpenClaw

Hermes logo

Hermes

Use Seqera MCP with Hermes

Atomic Agent logo

Atomic Agent

Use Seqera MCP with Atomic Agent

Google ADK logo

Google ADK

Use Seqera MCP with Google ADK

LangChain logo

LangChain

Use Seqera MCP with LangChain

Vercel AI SDK logo

Vercel AI SDK

Use Seqera MCP with Vercel AI SDK

Mastra AI logo

Mastra AI

Use Seqera MCP with Mastra AI

LlamaIndex logo

LlamaIndex

Use Seqera MCP with LlamaIndex

CrewAI logo

CrewAI

Use Seqera MCP with CrewAI

Pydantic AI logo

Pydantic AI

Use Seqera MCP with Pydantic AI

AutoGen logo

AutoGen

Use Seqera MCP with AutoGen

FAQ

Frequently asked questions

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.

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.

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.

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.

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