# How to integrate Seqera MCP with Claude Agent SDK

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

## Introduction

This guide walks you through connecting Seqera to the Claude Agent 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 Claude Agent 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

- [OpenAI Agents SDK](https://composio.dev/toolkits/seqera/framework/open-ai-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 Claude/Anthropic 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 Claude Agent SDK?

The Claude Agent SDK is Anthropic's official framework for building AI agents powered by Claude. It provides a streamlined interface for creating agents with MCP tool support and conversation management.
Key features include:
- Native MCP Support: Built-in support for Model Context Protocol servers
- Permission Modes: Control tool execution permissions
- Streaming Responses: Real-time response streaming for interactive applications
- Context Manager: Clean async context management for sessions

## 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 Claude/Anthropic API Key
- Primary know-how of Claude Agents SDK
- A Seqera account
- Some knowledge of Python

### 1. Getting API Keys for Claude/Anthropic and Composio

Claude/Anthropic API Key
- Go to the [Anthropic Console](https://console.anthropic.com/settings/organization/api-keys) and create an API key. You'll need credits to use the models.
- 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).
- Navigate to your API settings and generate a new API key.
- Store this key securely as you'll need it for authentication.

### 2. Install dependencies

No description provided.
```python
pip install composio-anthropic claude-agent-sdk python-dotenv
```

```typescript
npm install @anthropic-ai/claude-agent-sdk @composio/core dotenv
```

### 3. Set up environment variables

Create a .env file in your project root.
What's happening:
- COMPOSIO_API_KEY authenticates with Composio
- USER_ID identifies the user for session management
- ANTHROPIC_API_KEY authenticates with Anthropic/Claude
```bash
COMPOSIO_API_KEY=your_composio_api_key_here
USER_ID=your_user_id_here
ANTHROPIC_API_KEY=your_anthropic_api_key_here
```

### 4. Import dependencies

No description provided.
```python
import asyncio
from claude_agent_sdk import ClaudeSDKClient, ClaudeAgentOptions
import os
from composio import Composio
from dotenv import load_dotenv

load_dotenv()
```

```typescript
import 'dotenv/config';
import readline from 'node:readline';
import { Composio } from '@composio/core';
import { query, type Options } from "@anthropic-ai/claude-agent-sdk";

dotenv.config();
```

### 5. Create a Composio instance and Tool Router session

No description provided.
```python
async def chat_with_remote_mcp():
    api_key = os.getenv("COMPOSIO_API_KEY")
    if not api_key:
        raise RuntimeError("COMPOSIO_API_KEY is not set")

    composio = Composio(api_key=api_key)

    # Create Tool Router session for Seqera
    mcp_server = composio.create(
        user_id=os.getenv("USER_ID"),
        toolkits=["seqera"]
    )

    url = mcp_server.mcp.url

    if not url:
        raise ValueError("Session URL not found")
```

```typescript
async function chat() {
  const { COMPOSIO_API_KEY, USER_ID } = process.env;
  if (!COMPOSIO_API_KEY || !USER_ID) {
    throw new Error('COMPOSIO_API_KEY and USER_ID required in .env');
  }

  const composio = new Composio({ apiKey: COMPOSIO_API_KEY });

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

### 6. Configure Claude Agent with MCP

No description provided.
```python
# Configure remote MCP server for Claude
options = ClaudeAgentOptions(
    permission_mode="bypassPermissions",
    mcp_servers={
        "composio": {
            "type": "http",
            "url": url,
            "headers": {
                "x-api-key": os.getenv("COMPOSIO_API_KEY")
            }
        }
    },
    system_prompt="You are a helpful assistant with access to Seqera tools via Composio.",
    max_turns=10
)
```

```typescript
const options: Options = {
  permissionMode: 'bypassPermissions',
  mcpServers: {
    composio: {
      type: 'http',
      url: mcpUrl,
      headers: { 'x-api-key': COMPOSIO_API_KEY }
    }
  },
  systemPrompt: 'You are a helpful assistant with access to Seqera tools via Composio.',
  maxTurns: 10,
};
```

### 7. Create client and start chat loop

No description provided.
```python
# Create client with context manager
async with ClaudeSDKClient(options=options) as client:
    print("\nChat started. Type 'exit' or 'quit' to end.\n")

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

        # Send query
        await client.query(user_input)

        # Receive and print response
        print("Claude: ", end="", flush=True)
        async for message in client.receive_response():
            if hasattr(message, "content"):
                for block in message.content:
                    if hasattr(block, "text"):
                        print(block.text, end="", flush=True)
        print()
```

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

  console.log('\nChat started. Type "exit" to quit.\n');

  let isProcessing = false;

  async function ask(prompt: string) {
    isProcessing = true;
    rl.pause();

    process.stdout.write('Claude is thinking...');
    const stream = query({ prompt, options });

    let firstChunk = true;
    for await (const msg of stream) {
      const content = (msg as any).message?.content || (msg as any).content;
      if (Array.isArray(content)) {
        for (const block of content) {
          if (block.type === 'text' && block.text) {
            if (firstChunk) {
              process.stdout.write('\r\x1b[K');
              process.stdout.write('Claude: ');
              firstChunk = false;
            }
            process.stdout.write(block.text);
          }
        }
      }
    }
    process.stdout.write('\n\n');

    isProcessing = false;
    rl.resume();
    rl.prompt();
  }

  rl.on('line', async (line) => {
    if (isProcessing) return;

    const input = line.trim();
    if (input === 'exit') {
      rl.close();
      process.exit(0);
    }
    if (input) await ask(input);
    else rl.prompt();
  });

  await ask('What can you help me with?');
}
```

### 8. Run the application

No description provided.
```python
if __name__ == "__main__":
    asyncio.run(chat_with_remote_mcp())
```

```typescript
try {
  await chat();
} catch (error) {
  console.error(error);
  process.exit(1);
}
```

## Complete Code

```python
import asyncio
from claude_agent_sdk import ClaudeSDKClient, ClaudeAgentOptions
import os
from composio import Composio
from dotenv import load_dotenv

load_dotenv()

async def chat_with_remote_mcp():
    api_key = os.getenv("COMPOSIO_API_KEY")
    if not api_key:
        raise RuntimeError("COMPOSIO_API_KEY is not set")

    composio = Composio(api_key=api_key)

    # Create Tool Router session for Seqera
    mcp_server = composio.create(
        user_id=os.getenv("USER_ID"),
        toolkits=["seqera"]
    )

    url = mcp_server.mcp.url

    if not url:
        raise ValueError("Session URL not found")

    # Configure remote MCP server for Claude
    options = ClaudeAgentOptions(
        permission_mode="bypassPermissions",
        mcp_servers={
            "composio": {
                "type": "http",
                "url": url,
                "headers": {
                    "x-api-key": os.getenv("COMPOSIO_API_KEY")
                }
            }
        },
        system_prompt="You are a helpful assistant with access to Seqera tools via Composio.",
        max_turns=10
    )

    # Create client with context manager
    async with ClaudeSDKClient(options=options) as client:
        print("\nChat started. Type 'exit' or 'quit' to end.\n")

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

            # Send query
            await client.query(user_input)

            # Receive and print response
            print("Claude: ", end="", flush=True)
            async for message in client.receive_response():
                if hasattr(message, "content"):
                    for block in message.content:
                        if hasattr(block, "text"):
                            print(block.text, end="", flush=True)
            print()

if __name__ == "__main__":
    asyncio.run(chat_with_remote_mcp())
```

```typescript
import 'dotenv/config';
import readline from 'node:readline';
import { Composio } from '@composio/core';
import { query, type Options } from "@anthropic-ai/claude-agent-sdk";

async function chat() {
  const { COMPOSIO_API_KEY, USER_ID } = process.env;
  if (!COMPOSIO_API_KEY || !USER_ID) {
    throw new Error('COMPOSIO_API_KEY and USER_ID required in .env');
  }

  const composio = new Composio({ apiKey: COMPOSIO_API_KEY });
  const session = await composio.create(USER_ID, {
    toolkits: ['seqera']
  });
  const mcp_url = session?.mcp.url;

  const options: Options = {
    permissionMode: 'bypassPermissions',
    mcpServers: {
      composio: {
        type: 'http',
        url: mcp_url,
        headers: { 'x-api-key': COMPOSIO_API_KEY }
      }
    },
    systemPrompt: 'You are a helpful assistant with access to Seqera tools via Composio.',
    maxTurns: 10,
  };

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

  console.log('\nChat started. Type "exit" to quit.\n');

  let isProcessing = false;

  async function ask(prompt: string) {
    isProcessing = true;
    rl.pause();

    process.stdout.write('Claude is thinking...');
    const stream = query({ prompt, options });

    let firstChunk = true;
    for await (const msg of stream) {
      const content = (msg as any).message?.content || (msg as any).content;
      if (Array.isArray(content)) {
        for (const block of content) {
          if (block.type === 'text' && block.text) {
            if (firstChunk) {
              process.stdout.write('\r\x1b[K');
              process.stdout.write('Claude: ');
              firstChunk = false;
            }
            process.stdout.write(block.text);
          }
        }
      }
    }
    process.stdout.write('\n\n');

    isProcessing = false;
    rl.resume();
    rl.prompt();
  }

  rl.on('line', async (line) => {
    if (isProcessing) return;

    const input = line.trim();
    if (input === 'exit') {
      rl.close();
      process.exit(0);
    }
    if (input) await ask(input);
    else rl.prompt();
  });

  await ask('What can you help me with?');
}

try {
  await chat();
} catch (error) {
  console.error(error);
  process.exit(1);
}
```

## Conclusion

You've successfully built a Claude Agent SDK agent that can interact with Seqera through Composio's Tool Router.
Key features:
- Native MCP support through Claude's agent framework
- Streaming responses for real-time interaction
- Permission bypass for smooth automated workflows
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

- [OpenAI Agents SDK](https://composio.dev/toolkits/seqera/framework/open-ai-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)

## Related Toolkits

- [Excel](https://composio.dev/toolkits/excel) - Microsoft Excel is a robust spreadsheet application for organizing, analyzing, and visualizing data. It's the go-to tool for calculations, reporting, and flexible data management.
- [21risk](https://composio.dev/toolkits/_21risk) - 21RISK is a web app built for easy checklist, audit, and compliance management. It streamlines risk processes so teams can focus on what matters.
- [Abstract](https://composio.dev/toolkits/abstract) - Abstract provides a suite of APIs for automating data validation and enrichment tasks. It helps developers streamline workflows and ensure data quality with minimal effort.
- [Addressfinder](https://composio.dev/toolkits/addressfinder) - Addressfinder is a data quality platform for verifying addresses, emails, and phone numbers. It helps you ensure accurate customer and contact data every time.
- [Agentql](https://composio.dev/toolkits/agentql) - Agentql is a toolkit that connects AI agents to the web using a specialized query language. It enables structured web interaction and data extraction for smarter automations.
- [Agenty](https://composio.dev/toolkits/agenty) - Agenty is a web scraping and automation platform for extracting data and automating browser tasks—no coding needed. It streamlines data collection, monitoring, and repetitive online actions.
- [Ambee](https://composio.dev/toolkits/ambee) - Ambee is an environmental data platform providing real-time, hyperlocal APIs for air quality, weather, and pollen. Get precise environmental insights to power smarter decisions in your apps and workflows.
- [Ambient weather](https://composio.dev/toolkits/ambient_weather) - Ambient Weather is a platform for personal weather stations with a robust API for accessing local, real-time, and historical weather data. Get detailed environmental insights directly from your own sensors for smarter apps and automations.
- [Anonyflow](https://composio.dev/toolkits/anonyflow) - Anonyflow is a service for encryption-based data anonymization and secure data sharing. It helps organizations meet GDPR, CCPA, and HIPAA data privacy compliance requirements.
- [Api ninjas](https://composio.dev/toolkits/api_ninjas) - Api ninjas offers 120+ public APIs spanning categories like weather, finance, sports, and more. Developers use it to supercharge apps with real-time data and actionable endpoints.
- [Api sports](https://composio.dev/toolkits/api_sports) - Api sports is a comprehensive sports data platform covering 2,000+ competitions with live scores and 15+ years of stats. Instantly access up-to-date sports information for analysis, apps, or chatbots.
- [Apify](https://composio.dev/toolkits/apify) - Apify is a cloud platform for building, deploying, and managing web scraping and automation tools called Actors. It lets you automate data extraction and workflow tasks at scale—no infrastructure headaches.
- [Autom](https://composio.dev/toolkits/autom) - Autom is a lightning-fast search engine results data platform for Google, Bing, and Brave. Developers use it to access fresh, low-latency SERP data on demand.
- [Beaconchain](https://composio.dev/toolkits/beaconchain) - Beaconchain is a real-time analytics platform for Ethereum 2.0's Beacon Chain. It provides detailed insights into validators, blocks, and overall network performance.
- [Big data cloud](https://composio.dev/toolkits/big_data_cloud) - BigDataCloud provides APIs for geolocation, reverse geocoding, and address validation. Instantly access reliable location intelligence to enhance your applications and workflows.
- [Bigpicture io](https://composio.dev/toolkits/bigpicture_io) - BigPicture.io offers APIs for accessing detailed company and profile data. Instantly enrich your applications with up-to-date insights on 20M+ businesses.
- [Bitquery](https://composio.dev/toolkits/bitquery) - Bitquery is a blockchain data platform offering indexed, real-time, and historical data from 40+ blockchains via GraphQL APIs. Get unified, reliable access to complex on-chain data for analytics, trading, and research.
- [Brightdata](https://composio.dev/toolkits/brightdata) - Brightdata is a leading web data platform offering advanced scraping, SERP APIs, and anti-bot tools. It lets you collect public web data at scale, bypassing blocks and friction.
- [Builtwith](https://composio.dev/toolkits/builtwith) - BuiltWith is a web technology profiler that uncovers the technologies powering any website. Gain actionable insights into analytics, hosting, and content management stacks for smarter research and lead generation.
- [Byteforms](https://composio.dev/toolkits/byteforms) - Byteforms is an all-in-one platform for creating forms, managing submissions, and integrating data. It streamlines workflows by centralizing form data collection and automation.

## 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 Claude Agent SDK?

Yes, you can. Claude Agent 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.

---
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