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 your most recent session |
-s <session-id> | Resume a specific session by ID |
--approval-mode <mode> | Set the approval mode for local commands, for example basic 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 |
--sub-agent | Run as a subagent with structured JSONL output |
See Sessions for usage examples.
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--update | -u | Automatically update outdated skills |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 | Check only global installations | |
--local | Check only local (repository) installations |
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