Skip to main content

Overview of Seqera AI CLI

caution

Seqera AI is currently in beta. Features and commands may change as we continue to improve the product.

Seqera AI 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 the Seqera Platform.

Key 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.

How it works​

Seqera AI runs as a local CLI tool that connects to the Seqera AI backend service. When you start a session, the assistant has access to:

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

Getting started​

Install the CLI and start your first session in minutes:

# Install the CLI
pip install seqera-ai

# Login to your Seqera account
seqera login

# Start the AI assistant
seqera ai

See Getting started for a complete walkthrough.

Requirements​

  • Python 3.13 or later
  • A Seqera Platform account (sign up for free)
  • macOS, Linux, or Windows with WSL

Learn more​