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Skills configuration

Skills are reusable instruction sets that extend Co-Scientist with domain-specific workflows, prompts, and operating guidance.

Co-Scientist supports two skill workflows:

  • Session skills: SKILL.md files discovered from project and user skill directories and sent to the Co-Scientist backend as session context when you run seqera ai
  • Agent integrations: skill files installed by seqera skill install so other coding agents can invoke Co-Scientist as a subagent
tip

See Skills for a list of the available built-in skills and slash commands.

Use skills in the CLI​

When you start seqera ai, the CLI discovers available skills automatically. Backend-provided skills are also exposed as slash commands in the / command palette and /help.

You can:

  • Type / to browse built-in commands and backend skills
  • Run /help to see commands and skill descriptions in the terminal
  • Add project-specific SKILL.md files so Co-Scientist starts each session with the right context

Skill format​

Each skill lives in its own directory and includes a SKILL.md file with YAML frontmatter:

my-skill/
  SKILL.md
  references/
---
name: my-skill
description: Short description of what this skill does
---

Detailed instructions, examples, and guidelines.

name and description are required. Skills missing either field are skipped.

Discovery directories​

Co-Scientist searches these directories in order. The first directory to register a skill name takes precedence, and later skills with the same name are ignored.

PriorityPathScope
1<cwd>/.agents/skills/project
2<cwd>/.seqera/skills/project
3~/.agents/skills/user
4~/.seqera/skills/user
5~/.config/agents/skills/user
6~/.config/seqera/skills/user

Project skills take priority over user skills, so you can override a global skill with a repository-specific version.

Cross-agent compatibility​

.agents/skills/ follows the Agent Skills convention, which makes skills portable across coding agents. .seqera/skills/ is Seqera-specific.

Install skills into Co-Scientist​

You can add skills by creating the directory structure manually or by installing them from the Agent Skills ecosystem:

npx skills add https://github.com/vercel-labs/agent-skills --skill vercel-react-best-practices

After adding a skill, restart seqera ai so the new skill is loaded into the session.

Install Co-Scientist into coding agents​

Co-Scientist can install itself as a skill or instruction file so another coding agent can invoke it as a subagent. See Coding agents for the supported agents and the seqera skill install and seqera skill check commands.

Learn more​

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