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docs(seqera-ai): restructure skill docs and add code intelligence page
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‎platform-cloud/cloud-sidebar.json‎

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"seqera-ai/get-started",
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"seqera-ai/installation",
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"seqera-ai/authentication",
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"seqera-ai/use-cases",
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"seqera-ai/command-approval",
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"seqera-ai/skill",
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"seqera-ai/use-cases"
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"seqera-ai/skill-claude-code",
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"seqera-ai/skill-codex",
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"seqera-ai/skill-github-copilot",
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"seqera-ai/skill-other-agents",
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"seqera-ai/nextflow-lsp"
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]
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},
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{

‎platform-cloud/docs/seqera-ai/get-started.md‎

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1. Install the Seqera AI CLI:
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```bash
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pip install seqera
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npm install -g seqera
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```
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See [Installation](./installation.mdx) for a comprehensive installation guide.
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1. Run your first prompt:
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```
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/debug
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/debug-last-run-on-seqera
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```
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See [Use cases](./use-cases.md) for a comprehensive list of use cases.

‎platform-cloud/docs/seqera-ai/index.md‎

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- [Installation](./installation.mdx): Detailed installation instructions
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- [Authentication](./authentication.md): Log in, log out, and session management
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- [Command approval](./command-approval.md): Control which commands run automatically
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- [Skill for coding agents](./skill.md): Install Seqera AI as a skill for coding agents
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- [Working with Claude Code](./skill-claude-code.md): Install Seqera AI as a skill for Claude Code
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- [Working with Codex](./skill-codex.md): Install Seqera AI as a skill for Codex
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- [Working with GitHub Copilot](./skill-github-copilot.md): Install Seqera AI as a skill for GitHub Copilot
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- [Working with other coding agents](./skill-other-agents.md): Install Seqera AI for other coding agents
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- [Code intelligence](./nextflow-lsp.md): Language-server support in Seqera AI
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- [Use cases](./use-cases.md): Seqera AI CLI use cases
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- [Troubleshooting](../troubleshooting_and_faqs/seqera-ai.md): Troubleshoot common errors

‎platform-cloud/docs/seqera-ai/installation.mdx‎

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```
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:::info
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If you use Seqera AI as a [skill](./skill.md) for a coding agent, run `seqera skill check --update` after updating the CLI to keep your installed skills in sync with the current version. By default, this scans both local and global installations. Use `--global` or `--local` to narrow the scope.
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If you use Seqera AI as a skill for a coding agent, run `seqera skill check --update` after updating the CLI to keep your installed skills in sync with the current version. By default, this scans both local and global installations. Use `--global` or `--local` to narrow the scope. See [Working with Claude Code](./skill-claude-code.md), [Working with Codex](./skill-codex.md), [Working with GitHub Copilot](./skill-github-copilot.md), and [Working with other coding agents](./skill-other-agents.md).
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```bash
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seqera skill check --update

‎platform-cloud/docs/seqera-ai/nextflow-lsp.md‎

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---
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title: "Code intelligence"
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description: "Use language-server code intelligence features in Seqera AI"
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date: "2026-02-26"
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tags: [seqera-ai, cli, lsp, code-intelligence]
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---
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:::note
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Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [Contact us](https://seqera.io/platform/seqera-ai/request-credits/) for additional credits.
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:::
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When you ask Seqera AI to help with code in your workspace, it uses language server (LSP) context to provide:
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- Explanations for errors and warnings in your code
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- Context-aware completions and suggestions
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- Better navigation and understanding across project files
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For Nextflow projects, this includes diagnostics and code intelligence for scripts and config files.
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### Language support
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| LSP Server | Extensions | Requirements |
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|------------|------------|--------------|
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| Nextflow | `.nf`, `.config` | Java 17+ installed |
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| Python (Pyright) | `.py`, `.pyi` | Auto-installs |
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| R | `.r`, `.R`, `.rmd`, `.Rmd` | R runtime installed |
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LSP servers automatically start when you work with files that match these extensions.
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### Workspace detection
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Seqera AI detects the relevant language context from your active workspace and applies matching intelligence automatically.
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This means you can move between Nextflow, Python, and R files in the same project and get language-aware assistance without manual setup.
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See [Nextflow Language Server](https://github.com/nextflow-io/language-server) for advanced configuration details.
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### Learn more
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- [Seqera AI CLI](./index.md): Seqera AI overview
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- [Get started](./get-started.md): Start using Seqera AI
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- [Use cases](./use-cases.md): Seqera AI CLI use cases

‎platform-cloud/docs/seqera-ai/skill-claude-code.md‎

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---
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title: "Working with Claude Code"
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description: "Install and maintain the Seqera AI skill for Claude Code"
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date: "2026-02-26"
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tags: [seqera-ai, cli, skills, claude-code]
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---
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:::note
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Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [Contact us](https://seqera.io/platform/seqera-ai/request-credits/) for additional credits.
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:::
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The `seqera skill` command installs a skill file that enables [Claude Code](https://claude.ai/code) to use Seqera AI as a subagent. Once installed, Claude Code can invoke Seqera AI directly to manage workflows, build containers, query nf-core modules, and more without leaving your environment.
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### `seqera skill install`
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Install to the standard Claude Code location:
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```bash
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seqera skill install --path .claude/skills/
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```
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Or install to your home directory:
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```bash
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seqera skill install --global
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```
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You can also auto-detect and update an existing installation:
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```bash
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seqera skill install --detect
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```
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### Usage
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```bash
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seqera skill install [OPTIONS]
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```
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### Options
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| Option | Short | Description |
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|--------|-------|-------------|
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| `--path <PATH>` | `-p` | Install to a custom path (relative or absolute) |
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| `--global` | `-g` | Install to home directory |
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| `--detect` | `-d` | Auto-detect an existing installation and update it |
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### `seqera skill check`
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Verify that your installed skill matches your current CLI version:
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```bash
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seqera skill check
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```
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Update automatically if needed:
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```bash
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seqera skill check --update
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```
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### Usage
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```bash
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seqera skill check [OPTIONS]
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```
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### Options
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| Option | Short | Description |
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|--------|-------|-------------|
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| `--update` | `-u` | Automatically update outdated skills |
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| `--global` | | Check only global installations |
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| `--local` | | Check only local (repository) installations |
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### Learn more
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- [Use cases](./use-cases.md): Seqera AI CLI use cases
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- [Code intelligence](./nextflow-lsp.md): Language-aware coding support
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- [Installation](./installation.mdx): Detailed installation instructions

‎platform-cloud/docs/seqera-ai/skill-codex.md‎

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---
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title: "Working with Codex"
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description: "Install and maintain the Seqera AI skill for Codex"
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date: "2026-02-26"
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tags: [seqera-ai, cli, skills, codex]
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---
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:::note
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Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [Contact us](https://seqera.io/platform/seqera-ai/request-credits/) for additional credits.
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:::
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The `seqera skill` command installs a skill file that enables [Codex](https://openai.com/codex) to use Seqera AI as a subagent. Once installed, Codex can invoke Seqera AI directly to manage workflows, build containers, query nf-core modules, and more without leaving your environment.
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### `seqera skill install`
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Install to your project `AGENTS.md` path:
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```bash
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seqera skill install --path AGENTS.md
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```
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Or install to your home directory:
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```bash
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seqera skill install --global
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```
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You can also auto-detect and update an existing installation:
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```bash
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seqera skill install --detect
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```
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### Usage
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```bash
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seqera skill install [OPTIONS]
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```
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### Options
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| Option | Short | Description |
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|--------|-------|-------------|
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| `--path <PATH>` | `-p` | Install to a custom path (relative or absolute) |
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| `--global` | `-g` | Install to home directory |
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| `--detect` | `-d` | Auto-detect an existing installation and update it |
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### `seqera skill check`
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Verify that your installed skill matches your current CLI version:
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```bash
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seqera skill check
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```
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Update automatically if needed:
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```bash
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seqera skill check --update
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```
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### Usage
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```bash
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seqera skill check [OPTIONS]
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```
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### Options
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| Option | Short | Description |
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|--------|-------|-------------|
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| `--update` | `-u` | Automatically update outdated skills |
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| `--global` | | Check only global installations |
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| `--local` | | Check only local (repository) installations |
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### Learn more
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- [Use cases](./use-cases.md): Seqera AI CLI use cases
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- [Code intelligence](./nextflow-lsp.md): Language-aware coding support
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- [Installation](./installation.mdx): Detailed installation instructions

‎platform-cloud/docs/seqera-ai/skill-github-copilot.md‎

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---
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title: "Working with GitHub Copilot"
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description: "Install and maintain the Seqera AI skill for GitHub Copilot"
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date: "2026-02-26"
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tags: [seqera-ai, cli, skills, github-copilot]
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---
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:::note
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Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [Contact us](https://seqera.io/platform/seqera-ai/request-credits/) for additional credits.
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:::
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The `seqera skill` command installs a skill file that enables [GitHub Copilot](https://github.com/features/copilot) to use Seqera AI as a subagent. Once installed, GitHub Copilot can invoke Seqera AI directly to manage workflows, build containers, query nf-core modules, and more without leaving your environment.
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### `seqera skill install`
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Install to the standard Copilot instructions file:
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```bash
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seqera skill install --path .github/copilot-instructions.md
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```
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Or install to your home directory:
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```bash
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seqera skill install --global
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```
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You can also auto-detect and update an existing installation:
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```bash
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seqera skill install --detect
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```
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### Usage
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```bash
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seqera skill install [OPTIONS]
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```
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### Options
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| Option | Short | Description |
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|--------|-------|-------------|
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| `--path <PATH>` | `-p` | Install to a custom path (relative or absolute) |
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| `--global` | `-g` | Install to home directory |
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| `--detect` | `-d` | Auto-detect an existing installation and update it |
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### `seqera skill check`
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Verify that your installed skill matches your current CLI version:
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```bash
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seqera skill check
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```
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Update automatically if needed:
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```bash
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seqera skill check --update
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```
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### Usage
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```bash
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seqera skill check [OPTIONS]
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```
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### Options
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| Option | Short | Description |
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|--------|-------|-------------|
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| `--update` | `-u` | Automatically update outdated skills |
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| `--global` | | Check only global installations |
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| `--local` | | Check only local (repository) installations |
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### Learn more
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- [Use cases](./use-cases.md): Seqera AI CLI use cases
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- [Code intelligence](./nextflow-lsp.md): Language-aware coding support
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- [Installation](./installation.mdx): Detailed installation instructions

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