How to integrate Seqera MCP with Atomic Agent

Connect Atomic Agent 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

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 for installation instructions.

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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

  1. Sign up or sign in to the Composio dashboard. Copy your API key.
  2. 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.
  3. Ask Atomic Agent to do something in Seqera. It searches Composio for the right tool.
  4. 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.

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 or inspect the Atomic Agent source code.

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 for the current limits that apply to your connection.

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.

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. 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.

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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