Labcoat minimal bio code

Skill qchiujunhao/labcoat/skills/labcoat-minimal-bio-code

Skills, hooks, and CLI checks for safer biomedical AI coding agents.

Install

npx -y skills add qchiujunhao/labcoat --skill labcoat-minimal-bio-code

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Ponytail-style coding discipline for biomedical and bioinformatics code. Use when adding or reviewing biomedical code, dependencies, parsers, scripts, pipelines, or tests where minimal safe implementation and biological assumptions matter.

SKILL.md

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Minimal Bio Code

Build the smallest correct biomedical code path.

Decision Ladder

Reuse existing project helpers and domain libraries already present.
Use standard library for CLI, TOML, JSON, paths, subprocess, and text scanning.
Prefer mature existing parsers when already installed; do not hand-roll fragile biological formats unless the subset is explicit and tested.
Add a dependency only with a nearby labcoat-justification explaining why stdlib/current deps are insufficient.
Leave one focused test or self-check for non-trivial biomedical logic.

Allowed

Conservative heuristics with documented ceilings.
Explicit assumptions for genome build, species, input layer, units, and output contract.
Small scripts over custom frameworks for one workflow.

Disallowed

Do not invent biological assumptions to satisfy checks.
Do not add framework scaffolding for a single script.
Do not create custom parsers for VCF/BAM/FASTQ/GTF when an existing project dependency handles the format.
Do not add unnecessary dependencies.

Output

State the assumption, minimal implementation, test, and any deferred larger integration.

Read references/dependency-discipline.md before adding dependencies.