CLI
Reference for the seqera commands used with Co-Scientist. To install the CLI, see Installation. For the slash commands available inside a session, see Skills.
seqera login
Authenticate the CLI against your Seqera Platform account through a browser login.
seqera login
seqera logout
Sign out of the current session, revoke the authentication token, and remove locally stored credentials.
seqera logout
seqera ai
Start an interactive Co-Scientist session. Pass an optional initial query to begin with a prompt.
seqera ai [query] [options]
| Option | Description |
|---|---|
[query] | Optional initial prompt to start the session with |
-c, --continue | Continue your most recent session in the current directory |
-s, --session <session-id> | Resume a specific session by ID |
--approval-mode <mode> | Set the approval mode for local commands to basic, default, or full (see Command approval) |
--headless | Run non-interactively and send output to stdout |
--show-thinking | Include thinking messages in headless output |
--show-tools | Include tool calls in headless output |
--show-tool-results | Include tool results in headless output |
--sub-agent | Run as a subagent with structured JSONL output |
--events-path <file> | Write all session events to a file as JSONL |
-v, --verbose | Enable verbose logging |
--debug | Enable debug logging |
See Sessions for usage examples.
seqera info
Show the authenticated user, the agent backend, and Seqera Platform connection details. Use it to confirm that the CLI points at your Enterprise deployment.
seqera info [-o console|json]
| Option | Short | Description |
|---|---|---|
--output <format> | -o | Output format, console (default) or json |
seqera org
Manage your organization selection for billing.
| Command | Description |
|---|---|
seqera org | View your current organization |
seqera org list | List all organizations |
seqera org switch | Switch organization |
seqera org clear | Clear organization selection |
seqera skill install
Install Co-Scientist as a skill or instruction file for a coding agent.
seqera skill install [options]
| Option | Short | Description |
|---|---|---|
--local | -l | Install to repo root |
--path <PATH> | -p | Install to a custom path (relative or absolute) |
--global | -g | Install to home directory |
--detect | -d | Auto-detect an existing installation and update it |
seqera skill check
Verify that an installed skill matches your current CLI version.
seqera skill check [options]
| Option | Short | Description |
|---|---|---|
--update | -u | Automatically update outdated skills |
--global | -g | Check only global installations |
--local | -l | Check only local (repository) installations |
seqera update
Check for a newer CLI version and print the command to install it.
seqera update
seqera --version
Print the installed CLI version.
seqera --version
Learn more
- Installation: Install, update, and configure the CLI
- Sessions: Start, continue, resume, and exit sessions
- Coding agents: Install Co-Scientist as a skill in your coding agent
- Skills: Built-in skills, slash commands, and session limits
- Environment variables: Variables for authenticating and configuring the CLI