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Version: 26.1

Authentication

Co-Scientist uses your Seqera Platform account for authentication. This page describes authentication concepts and step-by-step instructions for managing your sessions.

Authenticating Co-Scientist​

Log in​

To authenticate with your Seqera Platform account, run:

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>

View session status​

To view your current session status, use the /status command inside the TUI:

/status

This shows your authentication status and organization details.

Add access tokens for automation​

For automated environments, you can provide a Seqera Platform access token directly using the SEQERA_ACCESS_TOKEN environment variable:

export SEQERA_ACCESS_TOKEN=<PLATFORM_ACCESS_TOKEN>
seqera ai

When this environment variable is set, the CLI skips the OAuth login flow and uses the provided token directly.

Connect to an Enterprise backend​

Set the following environment variables before starting seqera ai:

VariablePurposeExample value
SEQERA_AI_BACKEND_URLCo-Scientist backend endpoint used by the CLIhttps://ai-api.platform.example.com
SEQERA_AUTH_DOMAINOIDC authority base URL. The CLI fetches OpenID configuration from this URL and opens the discovered authorization endpoint in your browser.https://platform.example.com/api
SEQERA_AUTH_CLI_CLIENT_IDOAuth client ID for the Seqera CLIseqera_ai_cli
TOWER_ACCESS_TOKENPlatform personal access token used instead of browser login<PLATFORM_ACCESS_TOKEN>

Use the OAuth login flow:

export SEQERA_AUTH_DOMAIN=https://platform.example.com/api
export SEQERA_AUTH_CLI_CLIENT_ID=seqera_ai_cli
export SEQERA_AI_BACKEND_URL=https://ai-api.platform.example.com
seqera ai

Use a Platform personal access token instead of browser login:

export SEQERA_AUTH_DOMAIN=https://platform.example.com/api
export TOWER_ACCESS_TOKEN=<PLATFORM_ACCESS_TOKEN>
export SEQERA_AI_BACKEND_URL=https://ai-api.platform.example.com
seqera ai

Set SEQERA_AUTH_CLI_CLIENT_ID only for OAuth deployments that use a non-default CLI client ID. Current CLI builds still require SEQERA_AUTH_DOMAIN for Enterprise token-based authentication so the CLI can target the correct Platform authority.

Log out​

To sign out from the current session, run:

seqera logout

This command revokes your current authentication token and removes locally stored credentials. You will need to re-authenticate on next use.

Organization management​

The Seqera CLI supports managing your organization selection for billing. Use the seqera org command to view and switch organizations.

View current organization:

seqera org

List all organizations:

seqera org list

Switch organization:

seqera org switch

Clear organization selection:

seqera org clear

Token refresh​

The Seqera CLI automatically refreshes your authentication token when needed. You are not required to log in again unless:

  • You explicitly log out
  • Your refresh token expires (typically after extended inactivity)
  • Your Seqera Platform account permissions change

Learn more​

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