seqera-ai 0.1.0
Seqera AI CLI – Claude Code-like terminal assistant for bioinformatics and workflow management
License: Apache-2.0
Requires Python: >=3.13

# Seqera AI CLI

AI-powered assistant for bioinformatics workflows and Seqera Platform.

> ⚠️ **Beta Release**: Seqera AI CLI is currently in beta. Features and commands may change as we continue to improve the product.

> 💡 **Free Credits**: Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [Contact us](https://seqera.io/platform/seqera-ai/request-credits/) for additional credits.

Seqera AI CLI is an intelligent command-line assistant that helps you build, run, and manage bioinformatics workflows. Powered by advanced AI, it provides an interactive terminal experience for working with Nextflow pipelines and Seqera Platform.

Seqera AI has access to:

- **Your Seqera Platform workspace**: View and manage workflows, pipelines, and data through your authenticated account
- **Your local environment**: Execute commands and edit files in your working directory (with configurable approval controls)
- **AI capabilities**: Natural language understanding, code generation, and intelligent suggestions

## Installation

```bash
pip install seqera-ai
```

Or with pipx for isolated installation:

```bash
pipx install seqera-ai
```

## Quick Start

```bash
# Authenticate with Seqera Platform
seqera login

# Start the AI assistant
seqera ai
```

## Features

### Natural language interface

Interact with Seqera Platform using plain English. Ask questions, launch workflows, and manage pipelines through conversational commands.

### Workflow management

Launch, monitor, and debug Nextflow workflows directly from your terminal. Get real-time status updates, view logs, and analyze run metrics.

### Pipeline development

Generate Nextflow configurations, create pipeline schemas, and convert scripts from other workflow languages (WDL, Snakemake) to Nextflow.

### nf-core integration

Search and discover nf-core modules, get detailed execution information, and access ready-to-run Nextflow commands for over 1,000 standardized bioinformatics tools.

### Data management

Browse cloud storage through data links, manage datasets, generate download and upload URLs, and access reference genomes and sequencing data.

### Wave containers

Build containerized environments on-the-fly with conda packages, pip packages, or custom Docker images. Create reproducible containers for your bioinformatics tools without writing Dockerfiles.

### Local file operations

Edit files, run commands, and manage your local development environment with AI assistance and configurable approval modes.

### Seqera Platform integration

Full access to Platform capabilities including compute environments, datasets, data links, and workspace management.

## Usage

```bash
# Interactive mode (default)
seqera ai

# Single query mode
seqera ai "List my running workflows"

# With working directory
seqera ai -w /path/to/pipeline

# Show help
seqera --help
seqera ai --help
```

### Command approval modes

Control which commands run automatically with the `--approval-mode` flag:

| Mode      | Behavior                                                                                      |
| --------- | --------------------------------------------------------------------------------------------- |
| `basic`   | Only safe-list commands run automatically; everything else prompts for approval               |
| `default` | Safe-list commands and file edits within workdir run automatically; dangerous commands prompt |
| `full`    | Everything runs automatically unless on the dangerous list                                    |

```bash
# Start with basic approval mode
seqera ai --approval-mode basic

# Change mode during session
/approval basic
```

### Built-in commands

```bash
/                           Show available commands
/approval                   Show or set local approval mode
/schema                     Generate Nextflow schema
/debug                      Run pipeline diagnostics
/migrate-from-wdl           Migrate from WDL to Nextflow
/migrate-from-snakemake     Migrate from Snakemake to Nextflow
/write-nf-test              Write nf-tests for untested code
/debug-last-run             Debug last local run
/debug-last-run-on-seqera   Debug last Seqera Platform run
/clear                      Clear the conversation history
```

## Authentication

```bash
# Browser-based login (recommended)
seqera login

# Headless/device code flow
seqera login --device

# Check authentication status
seqera status

# Log out
seqera logout
```

## Requirements

- Python 3.13 or later
- Seqera Platform account

## Documentation

For detailed documentation, visit [seqera.io/docs](https://docs.seqera.io/).

## Support

- [Request additional credits](https://seqera.io/platform/seqera-ai/request-credits/)
- [Community support](https://community.seqera.io/)
- [Report issues](https://github.com/seqera-labs/seqera-ai/issues)

## License

Apache-2.0 License - see [LICENSE](LICENSE) file for details.