Skills

note

Seqera Cloud users receive $20 in free credits to get started with Seqera AI. Contact us for additional credits.

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

Seqera AI supports two skill workflows:

• CLI skills: SKILL.md files discovered from project and user skill directories and sent to the backend as session context
• Agent integrations: skill files installed by seqera skill install so other coding agents can invoke Seqera AI as a subagent

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 Seqera AI starts each session with the right context

Built-in skills

Your Seqera AI deployment can expose built-in skills as slash commands. These appear in the / command palette and in /help.

The CLI includes the following built-in skills by default:

Command	Description
/nextflow-config	Generate and explain Nextflow configuration files
/nextflow-schema	Generate nextflow_schema.json and sample sheet schema files
/debug-local-run	Debug a local Nextflow pipeline run using .nextflow.log, work directories, and related artifacts
/debug-last-run-on-seqera	Debug the last pipeline run on Seqera Platform
/convert-jupyter-notebook	Convert Jupyter notebooks to Nextflow pipelines
/convert-python-script	Convert Python scripts, including standalone scripts and Snakemake-style logic, to Nextflow
/convert-r-script	Convert R scripts to Nextflow pipelines
/fix-strict-syntax	Fix Nextflow strict syntax errors and help migrate pipelines to the v2 parser
/nf-aggregate	Aggregate metrics from Nextflow runs on Seqera Platform using the nf-aggregate pipeline
/nf-data-lineage	Explore Nextflow data lineage to trace which inputs and processes produced a result
/nf-pipeline-structure	Analyze a local Nextflow pipeline structure, including processes, workflows, modules, and channel flow
/nf-run-history	Analyze local Nextflow run history and summarize recent activity, progress, and recurring issues
/nf-schema-migration	Migrate Nextflow pipelines from nf-validation to nf-schema v2
/seqera-mcp	Access Seqera Platform through MCP tools for structured, validated operations
/seqera-platform-api	Query and manipulate Seqera Platform resources directly through the REST API
/seqerakit	Write seqerakit YAML configuration for automating Seqera Platform setup
/simplify	Review changed code for reuse, quality, and efficiency, then clean up issues found

note

The exact built-in skills available in your environment may vary by deployment and release. Use /help or type / in the CLI to see the current list.

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

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

Priority	Path	Scope
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 Seqera AI

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 Seqera AI into coding agents

Use seqera skill install to install Seqera AI as a skill or instruction file for another agent:

seqera skill install

Common installation flows:

seqera skill install --local
seqera skill install --global
seqera skill install --detect

Supported agents include:

Agent	Format
Claude Code	.claude/skills/
Codex	AGENTS.md
Cursor	.cursor/rules/
GitHub Copilot	.github/copilot-instructions.md
OpenCode	.opencode/
Pi	.pi/
Windsurf	.windsurf/rules/

Verify installed agent integrations with:

seqera skill check

Update outdated installations automatically:

seqera skill check --update

Payload limits

To keep session payloads small, Seqera AI caps discovered skill context at 5 KB. The total session payload cap is 20 KB.

Learn more

• Modes: Work in build mode, plan mode, and goal mode
• Working with Claude Code: Install Seqera AI as a skill for Claude Code
• Working with Codex: Install Seqera AI as a skill for Codex
• Working with GitHub Copilot: Install Seqera AI as a skill for GitHub Copilot
• Working with other coding agents: Install Seqera AI for other coding agents