bioinfo-sdd-spec-section

name: "bioinfo-sdd-spec-section" description: "Create or revise Bioinfo-skills analysis section specifications and section.yml contracts." compatibility: "Bioinfo-skills section SDD; Linux/Codex" metadata: author: "bioinfo-skills" source: "SPEC/bioinfo_native_section_sdd_plan.md"

Bioinfo SDD Spec Section

Use this skill when creating or revising spec.md and section.yml for a Bioinfo-skills analysis section.

Workflow

1. Read SPEC/bioinfo_native_section_sdd_plan.md.
2. Inspect declared pack_refs under sdd/packs/*/pack.yml before choosing workflow and task refs.
3. Treat package refs, tool refs, wrappers, and adapters as installed bundle outputs selected from tool_market/, not as pack-wide defaults.
4. Load the relevant entry/domain skill tree and stage skills referenced by the pack task template.
5. Keep section.yml as the machine-readable source of truth.
6. Ensure section.yml declares required gates, refs, allowed claims, forbidden claims, expected artifacts, and review status before Markdown artifacts expand on them.
7. In spec.md, state biological intent, required input state, produced output state, allowed claims, forbidden claims, and review gate status.
8. Run bioinfo-sdd validate-section <section_id> or PYTHONPATH=src python -m bioinfo_sdd validate-section <section_id>.
9. Stop at spec_review unless it is already approved.

Do not embed backend syntax in task or stage descriptions. Do not claim normalization, feature selection, PCA, annotation, condition inference, or biological interpretation unless the section explicitly implements and validates that state transition.