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Version: 26.1

Quickstart

This page walks you through your first Co-Scientist session: log in, start a session, switch between build mode and plan mode, debug a Platform run with a built-in skill, and set a long-running goal.

Prerequisites

You will need the following to get started:

  • Seqera CLI
  • A user account on your Seqera Platform Enterprise deployment
  • SEQERA_AI_BACKEND_URL set to your organization's agent backend (see Installation)

Step 1: Log in to Seqera Platform​

Authenticate the CLI against your Seqera Platform account:

seqera login

This will:

  1. Open your default browser to the Seqera login page.

  2. Prompt you to sign in with your Seqera Platform credentials.

  3. Automatically capture the authentication token.

  4. Display a success message in your terminal:

    [Login] Starting Seqera CLI authentication...
    [Login] ✓ Authentication successful!
    [Login] ✓ Organization set: <org_name>
tip

See Authentication for more information about how to log in and out, authenticate in automated environments, and manage your organization.

Step 2: Start an interactive session​

Launch an interactive Co-Scientist session:

seqera ai

The Co-Scientist prompt appears, with a footer showing the active mode (build by default). See Modes for more information.

Step 3: List commands and skills​

Show the built-in commands and available skills:

/help
tip

Type / to open command autocomplete.

Step 4: Switch between build and plan modes​

Co-Scientist runs in two modes that control what it can do:

  • Build mode (default): Executes commands, edits files, and launches workflows
  • Plan mode: Read-only analysis and planning, for exploring options before making changes

Press Shift+Tab to switch between modes. The active mode appears in the composer footer, and /status prints a full readout.

Try plan mode with a comparison prompt:

Compare whether I should add FastQC or fastp as the first QC step in this RNA-seq pipeline, including the workflow changes each option would require

Step 5: Debug a Seqera Platform run​

Run the built-in debugging skill against your most recent workspace run:

/debug-last-run-on-seqera

Co-Scientist fetches your most recent workspace run, inspects logs and exit codes, and walks through likely causes and fixes. You need at least one workflow run in the workspace for this skill to find something to debug.

Step 6: Set a long-running goal​

Give Co-Scientist a goal to work toward across multiple turns:

/goal update this pipeline for AWS Batch and add nf-tests

Co-Scientist works across model turns until the goal completes or the attempt limit is reached. See Use cases for more example prompts.

Learn more​

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