Seqera MCP for AI Agents

Securely connect your AI agents and chatbots (Claude, ChatGPT, Cursor, etc) with Seqera MCP or direct API to launch pipelines, monitor workflow runs, manage compute environments, and fetch status updates through natural language.

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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

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TOOL ROUTER PLAYGROUND
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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.

SETUP GUIDE

Connect Seqera MCP Tool with your Agent

1

Install Composio

typescript
npm install @composio/core ai @ai-sdk/openai @ai-sdk/mcp
Install the Composio SDK and Claude Agent SDK
2

Create Tool Router Session

typescript
import { Composio } from '@composio/core';

const composio = new Composio({ apiKey: 'your-api-key' });

console.log("Creating Tool Router session...");
const { mcp } = await composio.create('your-user-id');
console.log(`Tool Router session created: ${mcp.url}`);
Initialize the Composio client and create a Tool Router session
3

Connect to AI Agent

typescript
import { openai } from '@ai-sdk/openai';
import { experimental_createMCPClient as createMCPClient } from '@ai-sdk/mcp';
import { generateText, stepCountIs } from 'ai';

const client = await createMCPClient({
  transport: {
    type: 'http',
    url: mcp.url,
    headers: { 'x-api-key': 'your-composio-api-key' }
  }
});

const tools = await client.tools();

const { text } = await generateText({
  model: openai('gpt-4o'),
  tools,
  messages: [{ role: 'user', content: 'Launch a new Nextflow pipeline for RNA sequencing analysis' }],
  stopWhen: stepCountIs( 5 )
});

console.log(`Agent: ${text}`);
Use the MCP server with your AI agent
SETUP GUIDE

Connect Seqera API Tool with your Agent

1

Install Composio

typescript
npm install @composio/openai
Install the Composio SDK
2

Initialize Composio and Create Tool Router Session

typescript
import OpenAI from 'openai';
import { Composio } from '@composio/core';
import { OpenAIResponsesProvider } from '@composio/openai';

const composio = new Composio({
  provider: new OpenAIResponsesProvider(),
});
const openai = new OpenAI({});
const session = await composio.create('your-user-id');
Import and initialize Composio client, then create a Tool Router session
3

Execute Seqera Tools via Tool Router with Your Agent

typescript
const tools = session.tools;
const response = await openai.responses.create({
  model: 'gpt-4.1',
  tools: tools,
  input: [{
    role: 'user',
    content: 'Launch a new Nextflow pipeline for RNA sequencing analysis'
  }],
});
const result = await composio.provider.handleToolCalls(
  'your-user-id',
  response.output
);
console.log(result);
Get tools from Tool Router session and execute Seqera actions with your Agent

Why Use Composio?

AI Native Seqera Integration

  • Supports both Seqera MCP and direct API based integrations
  • Structured, LLM-friendly schemas for reliable tool execution
  • Rich coverage for launching, monitoring, and querying your Nextflow pipelines

Managed Auth

  • Built-in API key handling with secure storage
  • Central place to manage, scope, and revoke Seqera access
  • Per user and per environment credentials instead of hard-coded keys

Agent Optimized Design

  • Tools are tuned using real error and success rates to improve reliability over time
  • Comprehensive execution logs so you always know what ran, when, and on whose behalf

Enterprise Grade Security

  • Fine-grained RBAC so you control which agents and users can access Seqera
  • Scoped, least privilege access to Seqera resources
  • Full audit trail of agent actions to support review and compliance
FAQ

Frequently asked questions

Yes, Seqera requires you to configure your own API key credentials. Once set up, Composio handles secure credential storage and API request handling for you.

Yes! Composio's Tool Router enables agents to use multiple toolkits. Learn more.

Composio is SOC 2 and ISO 27001 compliant with all data encrypted in transit and at rest. Learn more.

Composio maintains and updates all toolkit integrations automatically, so your agents always work with the latest API versions.

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