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Antigravity/Gemini

The seqera skill command installs a skill file that enables Antigravity/Gemini to use Co-Scientist as a subagent. Once installed, Antigravity can invoke Co-Scientist directly to manage workflows, build containers, query nf-core modules, and more without leaving your environment.

This page covers the Antigravity skill format, how to install the skill automatically or by hand, the invocation patterns Antigravity uses, and how to keep the skill in sync as you update the CLI.

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.

AgentFormat
Antigravity/Gemini.agents/skills/

seqera skill install​

Use seqera skill install to add the Co-Scientist skill to Antigravity. Install it to the Antigravity skill directory, or pass another flag to choose a different location. If the installer can't write the skill, create it by hand with Manual installation.

Install to the Antigravity skill directory:

seqera skill install --path .agents/skills/seqera-ai-subagent/

Install into the current repository root:

seqera skill install --local

Or install to your home directory:

seqera skill install --global

You can also auto-detect and update an existing installation:

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 below.

Usage​

seqera skill install [OPTIONS]

Options​

seqera skill install accepts the following options:

OptionShortDescription
--local-lInstall to repo root
--path <PATH>-pInstall to a custom path (relative or absolute)
--global-gInstall to home directory
--detect-dAuto-detect an existing installation and update it

Manual installation​

If the automated installer does not support your agent platform, you can manually create the skill file:

  1. Create the skill directory:

    mkdir -p .agents/skills/seqera-ai-subagent/

  2. Create .agents/skills/seqera-ai-subagent/SKILL.md with the following content:

    ---
    name: seqera-ai-subagent
    description: Invokes Co-Scientist as a domain-expert subagent for Nextflow
    pipeline development, nf-core module management, Seqera Platform workspace
    operations, and Wave container builds.
    ---

    # Co-Scientist Subagent

    When the user asks about Nextflow pipelines, nf-core modules, Seqera Platform,
    or Wave containers, invoke Co-Scientist:

    seqera ai --headless --approval-mode basic "<query>" 2>&1

  3. Verify the installation:

    seqera skill check

Invocation patterns​

Antigravity invokes Co-Scientist dynamically via shell commands rather than static context injection. The recommended patterns are:

PatternCommandUse case
Headless queryseqera ai --headless --approval-mode basic "<query>"Read-only questions, analysis
Sub-agent modeseqera ai --sub-agent --approval-mode basic "<query>"Structured JSONL output
Goal modeseqera ai --headless --approval-mode full "/goal <task>"Multi-step autonomous work
Module QA reviewseqera ai --headless --approval-mode basic "Review modules/nf-core/<module>/main.nf for correctness"Pre-push nf-core module validation

Validated use case: nf-core module QA​

Antigravity uses Co-Scientist as a domain-expert QA gate before pushing nf-core module PRs. In PR #11377 (emmtyper), Co-Scientist 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.

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.

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:

OptionShortDescription
--update-uAutomatically update outdated skills
--globalCheck only global installations
--localCheck only local (repository) installations

Learn more​

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