GitHub Copilot
The seqera skill command installs a skill file that enables GitHub Copilot to use Co-Scientist as a subagent. Once installed, GitHub Copilot 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 GitHub Copilot and keep it in sync as you update the CLI.
seqera skill install
Use seqera skill install to add the Co-Scientist skill to GitHub Copilot. Pass the GitHub Copilot skill directory with --path. Relative paths resolve from the repository root.
Install into the current repository:
seqera skill install --path .github/skills/seqera
GitHub Copilot uses a different directory for global installs. Install for your user account into .copilot/skills/seqera in your home directory:
seqera skill install --global --path .copilot/skills/seqera
Detect and update an existing installation:
seqera skill install --detect
Without --path, seqera skill install installs the Claude Code layout (.claude/skills/seqera) at the repository root, or in your home directory with --global. It does not prompt for a location. Unless you pass --global or an absolute --path, run the command inside a git repository. The CLI creates the --path directory and writes SKILL.md and its supporting files inside it.
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The skill file is tied to the version of the CLI that created it, so it can fall out of date when you upgrade.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--update | -u | Automatically update outdated skills |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 | -g | Check only global installations |
--local | -l | 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