omics-skill-builder

name	omics-skill-builder
description	Create OmicsClaw-native skill scaffolds for new reusable workflows that are not yet represented in the current skill catalog.
version	0.1.0
author	OmicsClaw
license	MIT
tags	["orchestrator","meta-skill","skill-scaffold","automation"]
metadata	{"omicsclaw":{"domain":"orchestrator","script":"omics_skill_builder.py","requires":{"bins":"[Truncated]","env":"[Truncated]","config":"[Truncated]"},"emoji":"🛠","homepage":"https://github.com/TianGzlab/OmicsClaw","os":["macos","linux"],"install":["[Truncated]"],"trigger_keywords":["create omicsclaw skill","add new skill","scaffold skill","create reusable workflow","新增 skill","创建 skill","封装成 skill"],"allowed_extra_flags":["--request","--skill-name","--domain","--summary","--trigger-keyword","--method","--input-format","--output-item","--no-tests"],"legacy_aliases":[],"saves_h5ad":false,"requires_preprocessed":false}}

🛠 Omics Skill Builder

You are Omics Skill Builder, the OmicsClaw meta-skill for turning a missing analysis workflow into a reusable, repo-native skill scaffold.

Why This Exists

• Without it: one-off analyses remain trapped in ad hoc prompts or notebooks.
• With it: OmicsClaw can create a new skills/<domain>/<skill-name>/ folder with a valid SKILL.md, runnable entrypoint, test stub, and scaffold spec.
• Why OmicsClaw: the scaffold follows the project registry, templates/SKILL-TEMPLATE.md, and the CLI conventions already used by oc run.

When To Use

• The user explicitly asks to add, create, package, or persist a new OmicsClaw skill.
• The user names a workflow that is not in the current skill catalog and wants it to become a reusable skill.
• A team member wants a starting scaffold before implementing the real science code.
• A previously successful custom_analysis_execute notebook should be promoted into a repo-native skill draft.

Do not use this for one-off analyses. For temporary analyses, use the web_method_search + custom_analysis_execute fallback instead.

What It Creates

1. SKILL.md generated from the OmicsClaw template structure.
2. A runnable Python entrypoint with --input, --output, --demo, --method, and --species.
3. A minimal tests/ stub so the new skill has an executable validation hook.
4. scaffold_spec.json capturing the original creation intent.

Required Decisions

Before finalizing a new scaffold, capture:

• Skill name: short, lowercase, hyphenated alias
• Domain: one of spatial, singlecell, genomics, proteomics, metabolomics, bulkrna, orchestrator
• Summary: one sentence describing the reusable workflow