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Co-Scientist in Seqera CLI

Co-Scientist is Seqera's AI assistant for bioinformatics. You interact with it through the Seqera CLI (seqera ai) to build, run, and debug Nextflow pipelines, manage your data, and drive Seqera Platform from a single terminal session. It combines self-service bioinformatics, conversational intelligence, and autonomous execution in one experience.

Co-Scientist works across three contexts:

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

Get started​

To get started with Co-Scientist:

  1. Install Seqera CLI:

    npm install -g seqera

  2. Log in to Seqera:

    seqera login

  3. Start your first session:

    seqera ai

See Installation for prerequisites, updates, and development builds. Then see Quickstart to walk through your first session.

What you can do​

Co-Scientist helps across the full pipeline lifecycle, from writing code to running it on Seqera Platform:

Develop pipelines​

Generate Nextflow configurations and pipeline schemas, convert scripts from other languages (WDL, R) to Nextflow, and discover over 1,000 nf-core modules with ready-to-run commands. Build reproducible Wave containers from conda or pip packages without writing a Dockerfile. Real-time LSP code intelligence detects errors and powers AI navigation across Nextflow, Python, and R files.

Run and debug on Platform​

Launch, monitor, and debug Nextflow workflows from your terminal with real-time status, logs, and run metrics. Browse cloud storage through data links, manage datasets, generate upload and download URLs, and access reference genomes. Co-Scientist has full access to your compute environments, datasets, and workspace.

Work your way​

Interact in plain English, or use reusable skills exposed as slash commands in the / palette. Switch between build, plan, and goal modes to match execution, analysis, or long-running tasks. Resume earlier sessions with seqera ai -c, and organize workspace resources into projects using Platform labels.

Learn more​

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