skill-template

name	skill-template
description	Load when copying this directory to bootstrap a new OmicsClaw v2 skill (rename, fill in, then `git add`). Skip when an existing skill already covers the request.
version	0.1.0
author	OmicsClaw
license	MIT
tags	["template","scaffold","v2"]

REPLACE_SKILL_NAME

When to use

The user has <input shape> and wants <output shape>. Pick this skill when <distinguishing condition>. For <adjacent capability> use <sibling-skill> instead.

Inputs & Outputs

Input	Format	Required
Primary input	<.h5ad / .csv / .vcf / …>	yes (unless --demo)

Output	Path	Notes
Primary table	tables/<name>.csv	one row per <unit>
Report	report.md + result.json	always

Flow

1. Load input (--input <file>) or generate a demo (--demo).
2. Validate required columns / obs[X] keys; raise ValueError(...) early.
3. Run the chosen --method backend.
4. Write tables/<name>.csv (<script>.py:<L>) + report.md + result.json.

Gotchas

• None yet — append as failure modes are reported.

Key CLI

# Demo
python omicsclaw.py run REPLACE_SKILL_NAME --demo --output /tmp/REPLACE_SKILL_NAME_demo

# Real input
python omicsclaw.py run REPLACE_SKILL_NAME \
  --input <data.ext> --output results/ \
  --method <method-name>

See also

• references/parameters.md — every CLI flag, per-method tunables
• references/methodology.md — the WHY behind the algorithm
• references/output_contract.md — tables/X.csv + result.json schema
• Adjacent skills: <sibling-1> (upstream), <sibling-2> (parallel), <sibling-3> (downstream)