bioinfo-sdd-plan-section - SKILL.md Agent Skill

name: "bioinfo-sdd-plan-section" description: "Create or revise Bioinfo-skills analysis section implementation plans." compatibility: "Bioinfo-skills section SDD; Linux/Codex" metadata: author: "bioinfo-skills" source: "SPEC/bioinfo_native_section_sdd_plan.md"

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

Confirm spec_review is approved.
Read the section's pack_refs, workflow_ref, task_refs, package_refs, tool_refs, wrapper, adapter, and check_refs.
Resolve those IDs through sdd/packs/*/pack.yml.
Use bioinfo-sdd market-list --task-ref <task_id> and bioinfo-sdd market-show <bundle_id> before selecting concrete tools.
Install the chosen bundle with bioinfo-sdd install-tool-bundle <section_id> <bundle_id> or replace it with bioinfo-sdd replace-tool-bundle.
Treat bioinfo_tool as the active Bioinfo package/tool context only after the selected tool_market/ bundle has been installed into section-local installed_refs/.
Inspect only the relevant stage skills, installed package refs, installed tool refs, wrapper, and adapter files from the active installed-ref revision.
Do not load the full inactive tool_market/ as active planning context.
Document why the selected wrapper and adapter satisfy the declared input and output state without hidden preprocessing.
List high-impact parameters and keys written.
Run pack, market, installed-ref, and section checks: PYTHONPATH=src python -m bioinfo_sdd run-check market_manifest, PYTHONPATH=src python -m bioinfo_sdd run-check installed_refs --section <section_id>, and PYTHONPATH=src python -m bioinfo_sdd run-check section_catalog_links --section <section_id>.
Stop at plan_review unless it is already approved.

The plan should be replaceable: make it clear which choices come from the task template and which are section-local overrides.