omics-skill-builder

name	omics-skill-builder
description	Load when scaffolding a NEW OmicsClaw skill from a natural-language request — generates the skill directory layout (SKILL.md, parameters.yaml, references/, tests/) under the chosen domain. Skip when modifying an existing skill (edit its files directly) or when only routing a query (use `orchestrator`).
version	0.5.0
author	OmicsClaw
license	MIT
tags	["orchestrator","scaffold","skill-builder","meta","code-generation"]
requires	["pyyaml"]

omics-skill-builder

When to use

The user wants to add a NEW skill to the OmicsClaw catalog from a natural-language request. This skill produces a directory scaffold under the chosen --domain (spatial / singlecell / genomics / proteomics / metabolomics / bulkrna / orchestrator) with the v2 layout: SKILL.md, parameters.yaml, references/, tests/, plus a reproducibility manifest.

For modifying an existing skill, edit its files directly — this skill is for net-new additions only. For dispatching queries to existing skills, use orchestrator.

Inputs & Outputs

Input	Format	Required
User request	--request <text> (natural-language description of the desired skill)	yes (unless --demo)
Domain	--domain {spatial,singlecell,genomics,proteomics,metabolomics,bulkrna,orchestrator} (default orchestrator)	no
Skill alias	--skill-name <hyphenated>	no
Summary	--summary <one-line>	no
Promote source	--source-analysis-dir <path> or --promote-from-latest	no
Trigger keywords	--trigger-keyword <kw> (repeatable)	no
Methods / formats	--method <m> / --input-format <f> / --output-item <o> (each repeatable)	no
Skip tests	--no-tests	no

Output	Path	Notes
Scaffold summary	output_dir/SCAFFOLD_SUMMARY.md	what was generated, written at omics_skill_builder.py:129
Report	output_dir/report.md	written at omics_skill_builder.py:130
Reproducibility	output_dir/reproducibility/commands.sh	replay command, written at omics_skill_builder.py:132-137
Result envelope	output_dir/result.json	written at omics_skill_builder.py:139-141

Flow

1. Parse --request (or --demo); raise SystemExit("--request is required unless --demo is used.") at omics_skill_builder.py:75 when missing.
2. Optionally promote a previous autonomous-analysis output via --source-analysis-dir <path> or --promote-from-latest.
3. Call create_skill_scaffold (omicsclaw.core.skill_scaffolder); it writes the new skill directory under skills/<domain>/<skill-name>/.
4. Write SCAFFOLD_SUMMARY.md + report.md + reproducibility/commands.sh + result.json into --output.

Gotchas

• --request REQUIRED unless --demo — raises SystemExit (exit 1). omics_skill_builder.py:75 raises SystemExit("--request is required unless --demo is used."). Different from most OmicsClaw skills which use ValueError / parser.error; the exit code is 1, not 2.
• --domain defaults to orchestrator — usually NOT what you want. omics_skill_builder.py:30 defaults to orchestrator; pass --domain spatial (or whichever) explicitly. Choices are 7 fixed values; an unknown domain is rejected by argparse.
• The new skill is written to skills/<domain>/<skill-name>/, not --output. --output only receives the scaffold summary + report + commands.sh; the actual skill code goes under skills/. Don't confuse the two.
• --trigger-keyword, --method, --input-format, --output-item are REPEATABLE flags. Pass --trigger-keyword kw1 --trigger-keyword kw2 to add multiple. Single quoting won't help — argparse honours action="append".
• --promote-from-latest requires a recent autonomous-analysis output. If no recent output exists, the promotion silently no-ops.
• --demo lands in the orchestrator domain, NOT the implied target domain. omics_skill_builder.py:65 resolves domain = args.domain or "spatial", but args.domain defaults to "orchestrator" (truthy), so the demo scaffold is written to skills/orchestrator/spatial-cellcharter-domains/ rather than skills/spatial/.... For real scaffolds always pass --domain <target> explicitly.

Key CLI

# Demo (built-in scaffold example)
python omicsclaw.py run omics-skill-builder --demo --output /tmp/builder_demo

# Real scaffold for a spatial skill
python omicsclaw.py run omics-skill-builder \
  --request "Compute Moran's I per gene on Visium data" \
  --domain spatial --skill-name spatial-moran \
  --summary "Per-gene spatial autocorrelation via Moran's I" \
  --trigger-keyword "Moran" --trigger-keyword "spatial autocorrelation" \
  --method "moran-i" --input-format "h5ad" --output-item "tables/moran_per_gene.csv" \
  --output /tmp/scaffold_out

# Promote from a successful autonomous analysis
python omicsclaw.py run omics-skill-builder \
  --request "Promote the Moran analysis from yesterday into a real skill" \
  --domain spatial --source-analysis-dir /path/to/autonomous_run \
  --output /tmp/promoted

See also

• references/parameters.md — every CLI flag, repeatable behaviour
• references/methodology.md — scaffold layout, when to scaffold vs edit
• references/output_contract.md — SCAFFOLD_SUMMARY.md + result.json schema
• Adjacent skills: orchestrator (parallel — routes queries to EXISTING skills)