Claude Code
The seqera skill command installs a skill file that enables Claude Code to use Co-Scientist as a subagent. Once installed, Claude Code can invoke Co-Scientist directly to manage workflows, build containers, query nf-core modules, and more without leaving your environment.
This page covers how to install the skill into Claude Code and keep it in sync as you update the CLI.
seqera skill install
Use seqera skill install to add the Co-Scientist skill to Claude Code. Run it without options to launch an interactive installer that detects your setup and prompts for a location, or pass a flag to install directly to a specific path.
Launch the interactive installer:
seqera skill install
Install to the standard Claude Code location:
seqera skill install --path .claude/skills/
Install into the current repository root:
seqera skill install --local
Or install to your home directory:
seqera skill install --global
You can also auto-detect and update an existing installation:
seqera skill install --detect
Usage
seqera skill install [OPTIONS]
Options
seqera skill install accepts the following 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
The skill file is tied to the version of the CLI that created it, so it can fall out of date when you upgrade. Use seqera skill check to confirm your installed skill still matches your current CLI version, and update it when it doesn't.
Verify that your installed skill matches your current CLI version:
seqera skill check
Update automatically if needed:
seqera skill check --update
Usage
seqera skill check [OPTIONS]
Options
seqera skill check accepts the following options:
| Option | Short | Description |
|---|---|---|
--update | -u | Automatically update outdated skills |
--global | Check only global installations | |
--local | Check only local (repository) installations |
Learn more
- Installation: Install, update, and configure the CLI
- Quickstart: Run your first Co-Scientist session
- Authentication: Log in, log out, and manage sessions
- Use cases: Seqera CLI use cases
- Using Co-Scientist: Configure modes, sessions, skills, command approval, and more
- Coding Agents: Install Co-Scientist as a skill in your coding agent
- Skills: Built-in skills, slash commands, and session limits
- Troubleshooting: Troubleshoot common errors