How to integrate Seqera MCP with Hermes

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Introduction

Hermes is a 24/7 autonomous agent that lives on your computer or server — it remembers what it learns and evolves as your usage grows.

This guide explains the easiest and most robust way to connect your Seqera account to Hermes. You can do this through either Composio Connect CLI or Composio Connect MCP. For personal use we recommend the CLI, but you won't go wrong with MCP either.

Also integrate Seqera with

What is Composio Connect?

Composio Connect is a consumer offering that lets anyone plug 1,000+ applications directly into their agent harness — including Hermes. It can:

  • Search and load tools from relevant toolkits on-demand, reducing context usage.
  • Chain multiple tools to accomplish complex workflows via a remote workbench, without excessive back-and-forth with the LLM.
  • Manage app authentication end-to-end with zero manual overhead.

Integrating Seqera with Hermes

Using Composio Connect CLI

1. Install the Composio CLI

Run the install script directly, or paste https://composio.dev/hermes into your Hermes chat box to have it installed for you.

bash
curl -fsSL https://composio.dev/install | bash
Hermes authenticating with Composio

2. Authenticate

Once the CLI is installed, ask Hermes to authenticate with Composio.

3. Connect to Seqera

Ask your agent to connect to Seqera, or simply request any Seqera-related task. Hermes will prompt you to authenticate and authorize access.

4. Done. You're all set with a new Seqera connection.

Using Composio Connect MCP

1. Get your MCP URL and API Key

Go to dashboard.composio.dev and copy your Connect MCP URL and API key.

Copy MCP URL and API key from Composio dashboard

2. Open the Hermes config file

bash
nano ~/.hermes/config.yaml

3. Add the Composio Connect MCP server

bash
mcp_servers:
  composio:
    url: "https://connect.composio.dev/mcp"
    headers:
      x-consumer-api-key: "YOUR_COMPOSIO_API_KEY"
    connect_timeout: 60
    timeout: 180

Save with Ctrl + O, Enter, then exit with Ctrl + X.

4. Restart your Hermes agent

Once restarted, ask your agent to connect to Seqera or request any Seqera-related task. It will prompt you to authenticate and authorize access.

5. Done!

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

Way Forward

With Seqera connected, Hermes can now act on your behalf whenever it detects a relevant task or you ask it to.

From here, you can extend Hermes further:

  • Connect more apps: Calendar, Slack, Notion, Linear, and hundreds of others are available through the same Composio Connect setup. Each new integration compounds what Hermes can do for you.
  • Build workflows across tools: Once multiple apps are connected, Hermes can chain actions together — turn an email into a calendar invite, a Slack message into a Linear ticket, or a meeting note into a follow-up draft.
  • Let it learn your patterns: The more you use Hermes, the better it gets at anticipating how you'd handle recurring tasks. Give it feedback on drafts and decisions, and it will adapt.

If you run into trouble or want to share what you've built, join the community or check out the Docs for deeper configuration options.

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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 Hermes?

Yes, you can. Hermes 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
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Altera
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Context
Letta
glean
HubSpot
Agent.ai
Altera
DataStax
Entelligence
Rolai
Context
Letta
glean
HubSpot
Agent.ai
Altera
DataStax
Entelligence
Rolai

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