# How to integrate Seqera MCP with OpenAI Agents SDK

```json
{
  "title": "How to integrate Seqera MCP with OpenAI Agents SDK",
  "toolkit": "Seqera",
  "toolkit_slug": "seqera",
  "framework": "OpenAI Agents SDK",
  "framework_slug": "open-ai-agents-sdk",
  "url": "https://composio.dev/toolkits/seqera/framework/open-ai-agents-sdk",
  "markdown_url": "https://composio.dev/toolkits/seqera/framework/open-ai-agents-sdk.md",
  "updated_at": "2026-05-12T10:25:32.226Z"
}
```

## Introduction

This guide walks you through connecting Seqera to the OpenAI Agents SDK using the Composio tool router. By the end, you'll have a working Seqera agent that can launch a new nextflow pipeline run, monitor status of active pipeline jobs, list recent workflow execution logs through natural language commands.
This guide will help you understand how to give your OpenAI Agents SDK agent real control over a Seqera account through Composio's Seqera MCP server.
Before we dive in, let's take a quick look at the key ideas and tools involved.

## Also integrate Seqera with

- [Claude Agent SDK](https://composio.dev/toolkits/seqera/framework/claude-agents-sdk)
- [Claude Code](https://composio.dev/toolkits/seqera/framework/claude-code)
- [Claude Cowork](https://composio.dev/toolkits/seqera/framework/claude-cowork)
- [Codex](https://composio.dev/toolkits/seqera/framework/codex)
- [OpenClaw](https://composio.dev/toolkits/seqera/framework/openclaw)
- [Hermes](https://composio.dev/toolkits/seqera/framework/hermes-agent)
- [CLI](https://composio.dev/toolkits/seqera/framework/cli)
- [Google ADK](https://composio.dev/toolkits/seqera/framework/google-adk)
- [LangChain](https://composio.dev/toolkits/seqera/framework/langchain)
- [Vercel AI SDK](https://composio.dev/toolkits/seqera/framework/ai-sdk)
- [Mastra AI](https://composio.dev/toolkits/seqera/framework/mastra-ai)
- [LlamaIndex](https://composio.dev/toolkits/seqera/framework/llama-index)
- [CrewAI](https://composio.dev/toolkits/seqera/framework/crew-ai)

## TL;DR

Here's what you'll learn:
- Get and set up your OpenAI and Composio API keys
- Install the necessary dependencies
- Initialize Composio and create a Tool Router session for Seqera
- Configure an AI agent that can use Seqera as a tool
- Run a live chat session where you can ask the agent to perform Seqera operations

## What is OpenAI Agents SDK?

The OpenAI Agents SDK is a lightweight framework for building AI agents that can use tools and maintain conversation state. It provides a simple interface for creating agents with hosted MCP tool support.
Key features include:
- Hosted MCP Tools: Connect to external services through hosted MCP endpoints
- SQLite Sessions: Persist conversation history across interactions
- Simple API: Clean interface with Agent, Runner, and tool configuration
- Streaming Support: Real-time response streaming for interactive applications

## 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

| Tool slug | Name | Description |
|---|---|---|
| `SEQERA_CREATE_WAVE_CONTAINER` | Create Wave Container | Tool to submit a request to Wave for accessing a private container registry or building a container image on-the-fly. Use when you need to provision containers via Wave with Dockerfile, Conda recipe, or package specifications. Returns the name of the container made available by Wave. |
| `SEQERA_GET_ORGANIZATION_DETAILS` | Get Organization Details | Tool to retrieve detailed information about a specific organization. |
| `SEQERA_GET_SERVICE_INFO` | Get Service Info | Tool to retrieve information about the Seqera API service. Use when you need to check the service version and commit ID for troubleshooting. |
| `SEQERA_GET_USER_INFO` | Get User Info | Tool to retrieve information about the authenticated user. Use when you need to fetch details of the current user after authentication. |
| `SEQERA_GET_WAVE_BUILD_LOGS` | Get Wave Build Logs | Tool to get logs for a container build by build ID. Use when you need to troubleshoot or inspect the build process of a Wave container. |
| `SEQERA_GET_WAVE_BUILD_STATUS` | Get Wave Build Status | Tool to retrieve the status of a Wave container build by build ID. Use when you need to check if a container build is completed and whether it succeeded. |
| `SEQERA_INSPECT_WAVE_CONTAINER` | Inspect Wave Container | Tool to inspect container image metadata via Wave. Use when you need registry, manifest, digest, configuration, and OCI compatibility information about a container image. |
| `SEQERA_LIST_ACTION_EVENT_TYPES` | List Action Event Types | Tool to list supported action event types. Use when you need to discover available triggers for pipelines, optionally filtered by workspace. |
| `SEQERA_LIST_COMPUTE_ENVIRONMENTS` | List Compute Environments | Tool to retrieve a list of compute environments. Use when you need to page, sort, or filter compute environments accessible to your account. |
| `SEQERA_LIST_ORGANIZATIONS` | List Organizations | Tool to list all organizations. Use after authentication to retrieve accessible Seqera organizations. |
| `SEQERA_LIST_PIPELINES` | List Pipelines | Tool to list all pipelines accessible to the authenticated user. Use when you need to browse pipelines with optional pagination, sorting, or search filters. |
| `SEQERA_LIST_WORKFLOWS` | List Workflows | Tool to list workflows. Use when you need to retrieve workflows filtered by workspace and paginated. |
| `SEQERA_VALIDATE_ACTION_NAME` | Validate Action Name | Tool to validate action name. Use when you need to confirm if an action name is valid and available before creating an action. Returns validation status with details. |
| `SEQERA_VALIDATE_PIPELINE_NAME` | Validate Pipeline Name | Tool to validate a pipeline name. Use when you need to check if a given pipeline name is valid and available before creating or updating one. |

## Supported Triggers

None listed.

## Creating MCP Server - Stand-alone vs Composio SDK

The Seqera MCP server is an implementation of the Model Context Protocol that connects your AI agent to Seqera. It provides structured and secure access so your agent can perform Seqera operations on your behalf through a secure, permission-based interface.
With Composio's managed implementation, you don't have to create your own developer app. For production, if you're building an end product, we recommend using your own credentials. The managed server helps you prototype fast and go from 0-1 faster.

## Step-by-step Guide

### 1. Prerequisites

Before starting, make sure you have:
- Composio API Key and OpenAI API Key
- Primary know-how of OpenAI Agents SDK
- A live Seqera project
- Some knowledge of Python or Typescript

### 1. Getting API Keys for OpenAI and Composio

OpenAI API Key
- Go to the [OpenAI dashboard](https://platform.openai.com/settings/organization/api-keys) and create an API key. You'll need credits to use the models, or you can connect to another model provider.
- Keep the API key safe.
Composio API Key
- Log in to the [Composio dashboard](https://dashboard.composio.dev?utm_source=toolkits&utm_medium=framework_docs).
- Go to Settings and copy your API key.

### 2. Install dependencies

Install the Composio SDK and the OpenAI Agents SDK.
```python
pip install composio_openai_agents openai-agents python-dotenv
```

```typescript
npm install @composio/openai-agents @openai/agents dotenv
```

### 3. Set up environment variables

Create a .env file and add your OpenAI and Composio API keys.
```bash
OPENAI_API_KEY=sk-...your-api-key
COMPOSIO_API_KEY=your-api-key
USER_ID=composio_user@gmail.com
```

### 4. Import dependencies

What's happening:
- You're importing all necessary libraries.
- The Composio and OpenAIAgentsProvider classes are imported to connect your OpenAI agent to Composio tools like Seqera.
```python
import asyncio
import os
from dotenv import load_dotenv

from composio import Composio
from composio_openai_agents import OpenAIAgentsProvider
from agents import Agent, Runner, HostedMCPTool, SQLiteSession
```

```typescript
import 'dotenv/config';
import { Composio } from '@composio/core';
import { OpenAIAgentsProvider } from '@composio/openai-agents';
import { Agent, hostedMcpTool, run, OpenAIConversationsSession } from '@openai/agents';
import * as readline from 'readline';
```

### 5. Set up the Composio instance

No description provided.
```python
load_dotenv()

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

if not api_key:
    raise RuntimeError("COMPOSIO_API_KEY is not set. Create a .env file with COMPOSIO_API_KEY=your_key")

# Initialize Composio
composio = Composio(api_key=api_key, provider=OpenAIAgentsProvider())
```

```typescript
dotenv.config();

const composioApiKey = process.env.COMPOSIO_API_KEY;
const userId = process.env.USER_ID;

if (!composioApiKey) {
  throw new Error('COMPOSIO_API_KEY is not set. Create a .env file with COMPOSIO_API_KEY=your_key');
}
if (!userId) {
  throw new Error('USER_ID is not set');
}

// Initialize Composio
const composio = new Composio({
  apiKey: composioApiKey,
  provider: new OpenAIAgentsProvider(),
});
```

### 6. Create a Tool Router session

What is happening:
- You give the Tool Router the user id and the toolkits you want available. Here, it is only seqera.
- The router checks the user's Seqera connection and prepares the MCP endpoint.
- The returned session.mcp.url is the MCP URL that your agent will use to access Seqera.
- This approach keeps things lightweight and lets the agent request Seqera tools only when needed during the conversation.
```python
# Create a Seqera Tool Router session
session = composio.create(
    user_id=user_id,
    toolkits=["seqera"]
)

mcp_url = session.mcp.url
```

```typescript
// Create Tool Router session for Seqera
const session = await composio.create(userId as string, {
  toolkits: ['seqera'],
});
const mcpUrl = session.mcp.url;
```

### 7. Configure the agent

No description provided.
```python
# Configure agent with MCP tool
agent = Agent(
    name="Assistant",
    model="gpt-5",
    instructions=(
        "You are a helpful assistant that can access Seqera. "
        "Help users perform Seqera operations through natural language."
    ),
    tools=[
        HostedMCPTool(
            tool_config={
                "type": "mcp",
                "server_label": "tool_router",
                "server_url": mcp_url,
                "headers": {"x-api-key": api_key},
                "require_approval": "never",
            }
        )
    ],
)
```

```typescript
// Configure agent with MCP tool
const agent = new Agent({
  name: 'Assistant',
  model: 'gpt-5',
  instructions:
    'You are a helpful assistant that can access Seqera. Help users perform Seqera operations through natural language.',
  tools: [
    hostedMcpTool({
      serverLabel: 'tool_router',
      serverUrl: mcpUrl,
      headers: { 'x-api-key': composioApiKey },
      requireApproval: 'never',
    }),
  ],
});
```

### 8. Start chat loop and handle conversation

No description provided.
```python
print("\nComposio Tool Router session created.")

chat_session = SQLiteSession("conversation_openai_toolrouter")

print("\nChat started. Type your requests below.")
print("Commands: 'exit', 'quit', or 'q' to end\n")

async def main():
    try:
        result = await Runner.run(
            agent,
            "What can you help me with?",
            session=chat_session
        )
        print(f"Assistant: {result.final_output}\n")
    except Exception as e:
        print(f"Error: {e}\n")

    while True:
        user_input = input("You: ").strip()
        if user_input.lower() in {"exit", "quit", "q"}:
            print("Goodbye!")
            break

        result = await Runner.run(
            agent,
            user_input,
            session=chat_session
        )
        print(f"Assistant: {result.final_output}\n")

asyncio.run(main())
```

```typescript
// Keep conversation state across turns
const conversationSession = new OpenAIConversationsSession();

// Simple CLI
const rl = readline.createInterface({
  input: process.stdin,
  output: process.stdout,
  prompt: 'You: ',
});

console.log('\nComposio Tool Router session created.');
console.log('\nChat started. Type your requests below.');
console.log("Commands: 'exit', 'quit', or 'q' to end\n");

try {
  const first = await run(agent, 'What can you help me with?', { session: conversationSession });
  console.log(`Assistant: ${first.finalOutput}\n`);
} catch (e) {
  console.error('Error:', e instanceof Error ? e.message : e, '\n');
}

rl.prompt();

rl.on('line', async (userInput) => {
  const text = userInput.trim();

  if (['exit', 'quit', 'q'].includes(text.toLowerCase())) {
    console.log('Goodbye!');
    rl.close();
    process.exit(0);
  }

  if (!text) {
    rl.prompt();
    return;
  }

  try {
    const result = await run(agent, text, { session: conversationSession });
    console.log(`\nAssistant: ${result.finalOutput}\n`);
  } catch (e) {
    console.error('Error:', e instanceof Error ? e.message : e, '\n');
  }

  rl.prompt();
});

rl.on('close', () => {
  console.log('\n👋 Session ended.');
  process.exit(0);
});
```

## Complete Code

```python
import asyncio
import os
from dotenv import load_dotenv

from composio import Composio
from composio_openai_agents import OpenAIAgentsProvider
from agents import Agent, Runner, HostedMCPTool, SQLiteSession

load_dotenv()

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

if not api_key:
    raise RuntimeError("COMPOSIO_API_KEY is not set. Create a .env file with COMPOSIO_API_KEY=your_key")

# Initialize Composio
composio = Composio(api_key=api_key, provider=OpenAIAgentsProvider())

# Create Tool Router session
session = composio.create(
    user_id=user_id,
    toolkits=["seqera"]
)
mcp_url = session.mcp.url

# Configure agent with MCP tool
agent = Agent(
    name="Assistant",
    model="gpt-5",
    instructions=(
        "You are a helpful assistant that can access Seqera. "
        "Help users perform Seqera operations through natural language."
    ),
    tools=[
        HostedMCPTool(
            tool_config={
                "type": "mcp",
                "server_label": "tool_router",
                "server_url": mcp_url,
                "headers": {"x-api-key": api_key},
                "require_approval": "never",
            }
        )
    ],
)

print("\nComposio Tool Router session created.")

chat_session = SQLiteSession("conversation_openai_toolrouter")

print("\nChat started. Type your requests below.")
print("Commands: 'exit', 'quit', or 'q' to end\n")

async def main():
    try:
        result = await Runner.run(
            agent,
            "What can you help me with?",
            session=chat_session
        )
        print(f"Assistant: {result.final_output}\n")
    except Exception as e:
        print(f"Error: {e}\n")

    while True:
        user_input = input("You: ").strip()
        if user_input.lower() in {"exit", "quit", "q"}:
            print("Goodbye!")
            break

        result = await Runner.run(
            agent,
            user_input,
            session=chat_session
        )
        print(f"Assistant: {result.final_output}\n")

asyncio.run(main())
```

```typescript
import 'dotenv/config';
import { Composio } from '@composio/core';
import { OpenAIAgentsProvider } from '@composio/openai-agents';
import { Agent, hostedMcpTool, run, OpenAIConversationsSession } from '@openai/agents';
import * as readline from 'readline';

const composioApiKey = process.env.COMPOSIO_API_KEY;
const userId = process.env.USER_ID;

if (!composioApiKey) {
  throw new Error('COMPOSIO_API_KEY is not set. Create a .env file with COMPOSIO_API_KEY=your_key');
}
if (!userId) {
  throw new Error('USER_ID is not set');
}

// Initialize Composio
const composio = new Composio({
  apiKey: composioApiKey,
  provider: new OpenAIAgentsProvider(),
});

async function main() {
  // Create Tool Router session
  const session = await composio.create(userId as string, {
    toolkits: ['seqera'],
  });
  const mcpUrl = session.mcp.url;

  // Configure agent with MCP tool
  const agent = new Agent({
    name: 'Assistant',
    model: 'gpt-5',
    instructions:
      'You are a helpful assistant that can access Seqera. Help users perform Seqera operations through natural language.',
    tools: [
      hostedMcpTool({
        serverLabel: 'tool_router',
        serverUrl: mcpUrl,
        headers: { 'x-api-key': composioApiKey },
        requireApproval: 'never',
      }),
    ],
  });

  // Keep conversation state across turns
  const conversationSession = new OpenAIConversationsSession();

  // Simple CLI
  const rl = readline.createInterface({
    input: process.stdin,
    output: process.stdout,
    prompt: 'You: ',
  });

  console.log('\nComposio Tool Router session created.');
  console.log('\nChat started. Type your requests below.');
  console.log("Commands: 'exit', 'quit', or 'q' to end\n");

  try {
    const first = await run(agent, 'What can you help me with?', { session: conversationSession });
    console.log(`Assistant: ${first.finalOutput}\n`);
  } catch (e) {
    console.error('Error:', e instanceof Error ? e.message : e, '\n');
  }

  rl.prompt();

  rl.on('line', async (userInput) => {
    const text = userInput.trim();

    if (['exit', 'quit', 'q'].includes(text.toLowerCase())) {
      console.log('Goodbye!');
      rl.close();
      process.exit(0);
    }

    if (!text) {
      rl.prompt();
      return;
    }

    try {
      const result = await run(agent, text, { session: conversationSession });
      console.log(`\nAssistant: ${result.finalOutput}\n`);
    } catch (e) {
      console.error('Error:', e instanceof Error ? e.message : e, '\n');
    }

    rl.prompt();
  });

  rl.on('close', () => {
    console.log('\nSession ended.');
    process.exit(0);
  });
}

main().catch((err) => {
  console.error('Fatal error:', err);
  process.exit(1);
});
```

## Conclusion

This was a starter code for integrating Seqera MCP with OpenAI Agents SDK to build a functional AI agent that can interact with Seqera.
Key features:
- Hosted MCP tool integration through Composio's Tool Router
- SQLite session persistence for conversation history
- Simple async chat loop for interactive testing
You can extend this by adding more toolkits, implementing custom business logic, or building a web interface around the agent.

## How to build Seqera MCP Agent with another framework

- [Claude Agent SDK](https://composio.dev/toolkits/seqera/framework/claude-agents-sdk)
- [Claude Code](https://composio.dev/toolkits/seqera/framework/claude-code)
- [Claude Cowork](https://composio.dev/toolkits/seqera/framework/claude-cowork)
- [Codex](https://composio.dev/toolkits/seqera/framework/codex)
- [OpenClaw](https://composio.dev/toolkits/seqera/framework/openclaw)
- [Hermes](https://composio.dev/toolkits/seqera/framework/hermes-agent)
- [CLI](https://composio.dev/toolkits/seqera/framework/cli)
- [Google ADK](https://composio.dev/toolkits/seqera/framework/google-adk)
- [LangChain](https://composio.dev/toolkits/seqera/framework/langchain)
- [Vercel AI SDK](https://composio.dev/toolkits/seqera/framework/ai-sdk)
- [Mastra AI](https://composio.dev/toolkits/seqera/framework/mastra-ai)
- [LlamaIndex](https://composio.dev/toolkits/seqera/framework/llama-index)
- [CrewAI](https://composio.dev/toolkits/seqera/framework/crew-ai)

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## Frequently Asked Questions

### 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 OpenAI Agents SDK?

Yes, you can. OpenAI Agents SDK 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.

---
[See all toolkits](https://composio.dev/toolkits) · [Composio docs](https://docs.composio.dev/llms.txt)