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. Use --path to specify the Claude Code skill directory. Relative paths resolve from the repository root.

Install into the current repository:

seqera skill install --path .claude/skills/seqera

Install for your user account, relative to your home directory:

seqera skill install --global --path .claude/skills/seqera

Detect and update an existing installation:

seqera skill install --detect

note

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The skill file is tied to the version of the CLI that created it, so it can fall out of date when you upgrade.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--update	-u	Automatically update outdated skills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