# Seqera

```json
{
  "name": "Seqera",
  "slug": "seqera",
  "url": "https://composio.dev/toolkits/seqera",
  "markdown_url": "https://composio.dev/toolkits/seqera.md",
  "logo_url": "https://logos.composio.dev/api/seqera",
  "categories": [
    "data & analytics"
  ],
  "is_composio_managed": false,
  "updated_at": "2026-05-12T10:25:32.226Z"
}
```

![Seqera logo](https://logos.composio.dev/api/seqera)

## Description

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.

## Summary

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.

## Categories

- data & analytics

## Toolkit Details

- Tools: 14

## Images

- Logo: https://logos.composio.dev/api/seqera

## Authentication

- **Api Key**
  - Type: `api_key`
  - Description: Api Key authentication for Seqera.
  - Setup:
    - Configure Api Key credentials for Seqera.
    - Use the credentials when creating an auth config in Composio.

## Suggested Prompts

- Launch a new Nextflow pipeline run
- Monitor status of active pipeline jobs
- List recent workflow execution logs
- Scale compute environment for a pipeline

## 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.

## Installation and MCP Setup

### Path 1: SDK Installation

#### Path 1, Step 1: Install Composio

Install the Composio SDK
```python
pip install composio_openai
```

```typescript
npm install @composio/openai
```

#### Path 1, Step 2: Initialize Composio and Create Tool Router Session

Import and initialize Composio client, then create a Tool Router session
```python
from openai import OpenAI
from composio import Composio
from composio_openai import OpenAIResponsesProvider

composio = Composio(provider=OpenAIResponsesProvider())
openai = OpenAI()
session = composio.create(user_id='your-user-id')
```

```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');
```

#### Path 1, Step 3: Execute Seqera Tools via Tool Router with Your Agent

Get tools from Tool Router session and execute Seqera actions with your Agent
```python
tools = session.tools
response = openai.responses.create(
  model='gpt-4.1',
  tools=tools,
  input=[{
    'role': 'user',
    'content': 'Launch a new Nextflow pipeline for RNA sequencing analysis'
  }]
)
result = composio.provider.handle_tool_calls(
  response=response,
  user_id='your-user-id'
)
print(result)
```

```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);
```

### Path 2: MCP Server Setup

#### Path 2, Step 1: Install Composio

Install the Composio SDK and Claude Agent SDK
```python
pip install composio claude-agent-sdk
```

```typescript
npm install @composio/core ai @ai-sdk/openai @ai-sdk/mcp
```

#### Path 2, Step 2: Create Tool Router Session

Initialize the Composio client and create a Tool Router session
```python
from composio import Composio
from claude_agent_sdk import ClaudeSDKClient, ClaudeAgentOptions

composio = Composio(api_key='your-composio-api-key')
session = composio.create(user_id='your-user-id')
url = session.mcp.url
```

```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}`);
```

#### Path 2, Step 3: Connect to AI Agent

Use the MCP server with your AI agent
```python
import asyncio

options = ClaudeAgentOptions(
    permission_mode='bypassPermissions',
    mcp_servers={
        'tool_router': {
            'type': 'http',
            'url': url,
            'headers': {
                'x-api-key': 'your-composio-api-key'
            }
        }
    },
    system_prompt='You are a helpful assistant with access to Seqera tools.',
    max_turns=10
)

async def main():
    async with ClaudeSDKClient(options=options) as client:
        await client.query('Launch a new Nextflow pipeline for RNA sequencing analysis')
        async for message in client.receive_response():
            if hasattr(message, 'content'):
                for block in message.content:
                    if hasattr(block, 'text'):
                        print(block.text)

asyncio.run(main())
```

```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}`);
```

## Why Use Composio?

### 1. 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

### 2. 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

### 3. 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

### 4. 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

## Use Seqera with any AI Agent Framework

Choose a framework you want to connect Seqera with:

- [OpenAI Agents SDK](https://composio.dev/toolkits/seqera/framework/open-ai-agents-sdk)
- [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)
- [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)
- [Pydantic AI](https://composio.dev/toolkits/seqera/framework/pydantic-ai)
- [AutoGen](https://composio.dev/toolkits/seqera/framework/autogen)

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## Frequently Asked Questions

### Do I need my own developer credentials to use Seqera with Composio?

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.

### Can I use multiple toolkits together?

Yes! Composio's Tool Router enables agents to use multiple toolkits. [Learn more](https://docs.composio.dev/tool-router/overview).

### Is Composio secure?

Composio is SOC 2 and ISO 27001 compliant with all data encrypted in transit and at rest. [Learn more](https://trust.composio.dev).

### What if the API changes?

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

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