How to integrate Seqera MCP with Claude Code

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Introduction

Manage your Seqera directly from Claude Code with zero worries about OAuth hassles, API-breaking issues, or reliability and security concerns.

You can do this in two different ways:

  1. Via Composio Connect - Direct and easiest approach
  2. Via Composio SDK - Programmatic approach with more control

Also integrate Seqera with

Why use Composio?

  • Only one MCP URL to connect multiple apps with Claude Code with zero auth hassles.
  • Programmatic tool calling allows LLMs to write its code in a remote workbench to handle complex tool chaining. Reduces to-and-fro with LLMs for frequent tool calling.
  • Handling Large tool responses out of LLM context to minimize context rot.
  • Dynamic just-in-time access to 20,000 tools across 1000+ other Apps for cross-app workflows. It loads the tools you need, so LLMs aren't overwhelmed by tools you don't need.

Connecting Seqera to Claude Code using Composio

1. Add the Composio MCP to Claude

Terminal

2. Start Claude Code

bash
claude

3. Open your MCP list

bash
/mcp

4. Select Composio and click on Authenticate

Select Composio and click Authenticate

5. This will redirect you to the Composio OAuth page. Complete the flow by authorizing Composio and you're all set.

Composio OAuth authorization page
Composio authorization complete
Ask Claude to connect to your account and authenticate via the link

Supported Tools & Triggers

Tools
Create Wave ContainerTool to submit a request to Wave for accessing a private container registry or building a container image on-the-fly.
Get Organization DetailsTool to retrieve detailed information about a specific organization.
Get Service InfoTool to retrieve information about the Seqera API service.
Get User InfoTool to retrieve information about the authenticated user.
Get Wave Build LogsTool to get logs for a container build by build ID.
Get Wave Build StatusTool to retrieve the status of a Wave container build by build ID.
Inspect Wave ContainerTool to inspect container image metadata via Wave.
List Action Event TypesTool to list supported action event types.
List Compute EnvironmentsTool to retrieve a list of compute environments.
List OrganizationsTool to list all organizations.
List PipelinesTool to list all pipelines accessible to the authenticated user.
List WorkflowsTool to list workflows.
Validate Action NameTool to validate action name.
Validate Pipeline NameTool to validate a pipeline name.

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.

Connecting Seqera via Composio SDK

Composio SDK is the underlying tech that powers Rube. It's a universal gateway that does everything Rube does but with much more programmatic control. You can programmatically generate an MCP URL with the app you need (here Seqera) for even more tool search precision. It's secure and reliable.

How the Composio SDK works

The Composio SDK follows a three-phase workflow:

  1. Discovery: Searches for tools matching your task and returns relevant toolkits with their details.
  2. Authentication: Checks for active connections. If missing, creates an auth config and returns a connection URL via Auth Link.
  3. Execution: Executes the action using the authenticated connection.

Step-by-step Guide

Prerequisites

Before starting, make sure you have:
  • Claude Pro, Max, or API billing enabled Anthropic account
  • Composio API Key
  • A Seqera account
  • Basic knowledge of Python or TypeScript

Install Claude Code

bash
# macOS, Linux, WSL
curl -fsSL https://claude.ai/install.sh | bash

# Windows PowerShell
irm https://claude.ai/install.ps1 | iex

# Windows CMD
curl -fsSL https://claude.ai/install.cmd -o install.cmd && install.cmd && del install.cmd

To install Claude Code, use one of the following methods based on your operating system:

Set up Claude Code

bash
cd your-project-folder
claude

Open a terminal, go to your project folder, and start Claude Code:

  • Claude Code will open in your terminal
  • Follow the prompts to sign in with your Anthropic account
  • Complete the authentication flow
  • Once authenticated, you can start using Claude Code
Claude Code initial setup showing sign-in prompt
Claude Code terminal after successful login

Set up environment variables

bash
COMPOSIO_API_KEY=your_composio_api_key_here
USER_ID=your_user_id_here

Create a .env file in your project root with the following variables:

  • COMPOSIO_API_KEY authenticates with Composio (get it from Composio dashboard)
  • USER_ID identifies the user for session management (use any unique identifier)

Install Composio library

pip install composio-core python-dotenv

Install the Composio Python library to create MCP sessions.

  • composio-core provides the core Composio functionality
  • python-dotenv loads environment variables from your .env file

Generate Composio MCP URL

import os
from composio import Composio
from dotenv import load_dotenv

load_dotenv()

COMPOSIO_API_KEY = os.getenv("COMPOSIO_API_KEY")
USER_ID = os.getenv("USER_ID")

composio_client = Composio(api_key=COMPOSIO_API_KEY)

composio_session = composio_client.create(
    user_id=USER_ID,
    toolkits=["seqera"],
)

COMPOSIO_MCP_URL = composio_session.mcp.url

print(f"MCP URL: {COMPOSIO_MCP_URL}")
print(f"\nUse this command to add to Claude Code:")
print(f'claude mcp add --transport http seqera-composio "{COMPOSIO_MCP_URL}" --headers "X-API-Key:{COMPOSIO_API_KEY}"')

Create a script to generate a Composio MCP URL for Seqera. This URL will be used to connect Claude Code to Seqera.

What's happening:
  • We import the Composio client and load environment variables
  • Create a Composio instance with your API key
  • Call create() to create a Tool Router session for Seqera
  • The returned mcp.url is the MCP server URL that Claude Code will use
  • The script prints this URL so you can copy it

Run the script and copy the MCP URL

python generate_mcp_url.py

Run your Python script to generate the MCP URL.

  • The script connects to Composio and creates a Tool Router session
  • It prints the MCP URL and the exact command you need to run
  • Copy the entire claude mcp add command from the output

Add Seqera MCP to Claude Code

bash
claude mcp add --transport http seqera-composio "YOUR_MCP_URL_HERE" --headers "X-API-Key:YOUR_COMPOSIO_API_KEY"

# Then restart Claude Code
exit
claude

In your terminal, add the MCP server using the command from the previous step. The command format is:

  • claude mcp add registers a new MCP server with Claude Code
  • --transport http specifies that this is an HTTP-based MCP server
  • The server name (seqera-composio) is how you'll reference it
  • The URL points to your Composio Tool Router session
  • --headers includes your Composio API key for authentication

After running the command, close the current Claude Code session and start a new one for the changes to take effect.

Verify the installation

bash
claude mcp list

Check that your Seqera MCP server is properly configured.

  • This command lists all MCP servers registered with Claude Code
  • You should see your seqera-composio entry in the list
  • This confirms that Claude Code can now access Seqera tools

If everything is wired up, you should see your seqera-composio entry listed:

Claude Code MCP list showing the toolkit MCP server

Authenticate Seqera

The first time you try to use Seqera tools, you'll be prompted to authenticate.

  • Claude Code will detect that you need to authenticate with Seqera
  • It will show you an authentication link
  • Open the link in your browser (or copy/paste it)
  • Complete the Seqera authorization flow
  • Return to the terminal and start using Seqera through Claude Code

Once authenticated, you can ask Claude Code to perform Seqera operations in natural language. For example:

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

Complete Code

Here's the complete code to get you started with Seqera and Claude Code:

import os
from composio import Composio
from dotenv import load_dotenv

load_dotenv()

COMPOSIO_API_KEY = os.getenv("COMPOSIO_API_KEY")
USER_ID = os.getenv("USER_ID")

composio_client = Composio(api_key=COMPOSIO_API_KEY)

composio_session = composio_client.create(
    user_id=USER_ID,
    toolkits=["seqera"],
)

COMPOSIO_MCP_URL = composio_session.mcp.url

print(f"MCP URL: {COMPOSIO_MCP_URL}")
print(f"\nUse this command to add to Claude Code:")
print(f'claude mcp add --transport http seqera-composio "{COMPOSIO_MCP_URL}" --headers "X-API-Key:{COMPOSIO_API_KEY}"')

Conclusion

You've successfully integrated Seqera with Claude Code using Composio's MCP server. Now you can interact with Seqera directly from your terminal using natural language commands.

Key features of this setup:

  • Terminal-native experience without switching contexts
  • Natural language commands for Seqera operations
  • Secure authentication through Composio's managed MCP
  • Tool Router for dynamic tool discovery and execution

Next steps:

  • Try asking Claude Code to perform various Seqera operations
  • Add more toolkits to your Tool Router session for multi-app workflows
  • Integrate this setup into your development workflow for increased productivity

You can extend this by adding more toolkits, implementing custom workflows, or building automation scripts that leverage Claude Code's capabilities.

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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 Code?

Yes, you can. Claude Code 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.

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