From 96ce16d797fcd2855b18060f54f59564e9f50090 Mon Sep 17 00:00:00 2001 From: "Harrison H. Vaughn Reed" Date: Wed, 29 Apr 2026 11:30:28 -0400 Subject: [PATCH 1/2] docs: Add Antigravity/Gemini as a supported agent for Seqera AI skills Add skill-antigravity.md documenting how to install and use Seqera AI as a subagent within Google's Antigravity/Gemini IDE. This is the first integration between Antigravity and Seqera AI, using the portable .agents/skills/ Agent Skills convention. Includes: - Installation via seqera skill install --path .agents/skills/ - Manual installation fallback for unsupported CLI targets - Headless, sub-agent, and goal-mode invocation patterns - Navigation link added to index.md Created during the nf-core Boston Hackathon 2026. --- platform-cloud/docs/seqera-ai/index.md | 1 + .../docs/seqera-ai/skill-antigravity.md | 141 ++++++++++++++++++ 2 files changed, 142 insertions(+) create mode 100644 platform-cloud/docs/seqera-ai/skill-antigravity.md diff --git a/platform-cloud/docs/seqera-ai/index.md b/platform-cloud/docs/seqera-ai/index.md index e83fd6481..6dcf78eba 100644 --- a/platform-cloud/docs/seqera-ai/index.md +++ b/platform-cloud/docs/seqera-ai/index.md @@ -85,6 +85,7 @@ Organize a workspace into projects by applying Seqera Platform labels prefixed w - [Working with Claude Code](./skill-claude-code.md): Install Seqera AI as a skill for Claude Code - [Working with Codex](./skill-codex.md): Install Seqera AI as a skill for Codex - [Working with GitHub Copilot](./skill-github-copilot.md): Install Seqera AI as a skill for GitHub Copilot +- [Working with Antigravity/Gemini](./skill-antigravity.md): Install Seqera AI as a skill for Antigravity/Gemini - [Working with other coding agents](./skill-other-agents.md): Install Seqera AI for other coding agents - [Code intelligence](./nextflow-lsp.md): Language-server support in Seqera AI - [Use cases](./use-cases.md): Seqera AI CLI use cases diff --git a/platform-cloud/docs/seqera-ai/skill-antigravity.md b/platform-cloud/docs/seqera-ai/skill-antigravity.md new file mode 100644 index 000000000..036322f2d --- /dev/null +++ b/platform-cloud/docs/seqera-ai/skill-antigravity.md @@ -0,0 +1,141 @@ +--- +title: "Working with Antigravity/Gemini" +description: "Install and maintain the Seqera AI skill for Google's Antigravity/Gemini IDE" +date created: "2026-04-29" +tags: [seqera-ai, cli, skills, antigravity, gemini] +--- + +:::note +Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [Contact us](https://seqera.io/platform/seqera-ai/request-credits/) for additional credits. +::: + +The `seqera skill` command installs a skill file that enables [Antigravity/Gemini](https://blog.google/technology/google-deepmind/gemini-model-thinking-updates-march-2025/) to use Seqera AI as a subagent. Once installed, Antigravity can invoke Seqera AI directly to manage workflows, build containers, query nf-core modules, and more without leaving your environment. + +### Antigravity/Gemini skill format + +Antigravity/Gemini discovers skills from the `.agents/skills/` directory at the repository root. Each skill is a folder containing a `SKILL.md` file with YAML frontmatter (name, description) and detailed instructions. + +| Agent | Format | +|-------|--------| +| [Antigravity/Gemini](https://blog.google/technology/google-deepmind/) | `.agents/skills/` | + +### `seqera skill install` + +Install to the Antigravity skill directory: + +```bash +seqera skill install --path .agents/skills/seqera-ai-subagent/ +``` + +Install into the current repository root: + +```bash +seqera skill install --local +``` + +Or install to your home directory: + +```bash +seqera skill install --global +``` + +You can also auto-detect and update an existing installation: + +```bash +seqera skill install --detect +``` + +:::note +If you encounter a `ENOENT: no such file or directory, scandir '/$bunfs/root/content/seqera'` error with `seqera skill install`, you can manually create the skill file. See [Manual installation](#manual-installation) below. +::: + +### Manual installation + +If the automated installer does not support your agent platform, you can manually create the skill file: + +1. Create the skill directory: + ```bash + mkdir -p .agents/skills/seqera-ai-subagent/ + ``` + +2. Create `.agents/skills/seqera-ai-subagent/SKILL.md` with the following content: + ```markdown + --- + name: seqera-ai-subagent + description: Invokes the Seqera AI CLI as a domain-expert subagent for Nextflow + pipeline development, nf-core module management, Seqera Platform workspace + operations, and Wave container builds. + --- + + # Seqera AI Subagent + + When the user asks about Nextflow pipelines, nf-core modules, Seqera Platform, + or Wave containers, invoke the Seqera AI CLI: + + seqera ai --headless --approval-mode basic "" 2>&1 + ``` + +3. Verify the installation: + ```bash + seqera skill check + ``` + +### Invocation patterns + +Antigravity invokes Seqera AI dynamically via shell commands rather than static context injection. The recommended patterns are: + +| Pattern | Command | Use case | +|---------|---------|----------| +| Headless query | `seqera ai --headless --approval-mode basic ""` | Read-only questions, analysis | +| Sub-agent mode | `seqera ai --sub-agent --approval-mode basic ""` | Structured JSONL output | +| Goal mode | `seqera ai --headless --approval-mode full "/goal "` | Multi-step autonomous work | + +### Usage + +```bash +seqera skill install [OPTIONS] +``` + +### Options + +| Option | Short | Description | +|--------|-------|-------------| +| `--local` | `-l` | Install to repo root | +| `--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` + +Verify that your installed skill matches your current CLI version: + +```bash +seqera skill check +``` + +Update automatically if needed: + +```bash +seqera skill check --update +``` + +### Usage + +```bash +seqera skill check [OPTIONS] +``` + +### Options + +| Option | Short | Description | +|--------|-------|-------------| +| `--update` | `-u` | Automatically update outdated skills | +| `--global` | | Check only global installations | +| `--local` | | Check only local (repository) installations | + +### Learn more + +- [Skills](./skills.md): Discover, create, and install skills +- [Use cases](./use-cases.md): Seqera AI CLI use cases +- [Code intelligence](./nextflow-lsp.md): Language-aware coding support +- [Installation](./installation.md): Detailed installation instructions From 90d45cb03b9c7d9db29291d4385d21be072b3534 Mon Sep 17 00:00:00 2001 From: "Harrison H. Vaughn Reed" Date: Wed, 29 Apr 2026 12:43:19 -0400 Subject: [PATCH 2/2] docs(skill-antigravity): Add Module QA Review pattern and validated use case Added the nf-core module QA review invocation pattern, validated during PR #11377 (emmtyper). Seqera AI caught Click version fragility and recommended python -c import for robust cross-environment version extraction. --- platform-cloud/docs/seqera-ai/skill-antigravity.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/platform-cloud/docs/seqera-ai/skill-antigravity.md b/platform-cloud/docs/seqera-ai/skill-antigravity.md index 036322f2d..a83e87201 100644 --- a/platform-cloud/docs/seqera-ai/skill-antigravity.md +++ b/platform-cloud/docs/seqera-ai/skill-antigravity.md @@ -89,6 +89,18 @@ Antigravity invokes Seqera AI dynamically via shell commands rather than static | Headless query | `seqera ai --headless --approval-mode basic ""` | Read-only questions, analysis | | Sub-agent mode | `seqera ai --sub-agent --approval-mode basic ""` | Structured JSONL output | | Goal mode | `seqera ai --headless --approval-mode full "/goal "` | Multi-step autonomous work | +| Module QA review | `seqera ai --headless --approval-mode basic "Review modules/nf-core//main.nf for correctness"` | Pre-push nf-core module validation | + +### Validated use case: nf-core module QA + +Antigravity uses Seqera AI as a domain-expert QA gate before pushing nf-core module PRs. In [PR #11377](https://github.com/nf-core/modules/pull/11377) (emmtyper), Seqera AI caught that `emmtyper --version | sed` was fragile across Docker/Conda environments due to Click version differences, and recommended using `python -c "import emmtyper; print(emmtyper.__version__)"` instead. + +```bash +seqera ai --headless --approval-mode basic \ + "Review modules/nf-core/emmtyper/main.nf for topic channel, stub, and eval correctness" 2>&1 +``` + +This pattern complements `nf-core modules lint` by catching semantic issues that static linting misses. ### Usage