| Convert a taxonomy (`outline/taxonomy.yml`) into a bullet-only outline (`outline/outline.yml`) with sections/subsections.
npx skills add https://github.com/WILLOSCAR/research-units-pipeline-skills --skill outline-builder
outline/outline.refined.ok freezes a reviewed outline only while the marker is newer than the outline, all declared inputs, the defaults asset, and the generator. Upstream changes invalidate the marker and trigger a backed-up regeneration.
Build outline/outline.yml from either:
outline/taxonomy.yml (legacy H3-first compatibility path)outline/chapter_skeleton.yml + outline/section_briefs.jsonl (section-first transition path)Compatibility mode is active: this migration keeps the current output contract while moving intro/related defaults, Stage A bullet templates, and domain-specific comparison framing into references/ and assets/.
Always read:
references/overview.mdreferences/stage_a_contract.mdRead by task:
references/intro_related_patterns.md when changing Introduction / Related Work defaultsreferences/examples_good.md and references/examples_bad.md for bullet calibrationMachine-readable asset:
assets/outline_defaults.yamlRequired:
outline/taxonomy.ymlOptional human calibration only:
ref/agent-surveys/STYLE_REPORT.mdref/agent-surveys/text/Keep the current output contract:
outline/outline.ymlCurrent mode is reference-first with script compatibility:
assets/outline_defaults.yamlassets/outline_defaults.yamlreferences/scripts/run.py still owns outline materialization, section-first input selection, and placeholder-safe overwrite behaviorUse scripts/run.py only for:
Do not treat the script as the main place for:
Introduction / Related WorkKeep these stable:
outline/outline.yml is a YAML listIntroduction and Related Work remain the first two H2 sectionsIntent: / RQ: / Evidence needs: / Expected cites:uv run python .codex/skills/outline-builder/scripts/run.py --helpuv run python .codex/skills/outline-builder/scripts/run.py --workspace <workspace>When running this skill in compatibility mode, scripts/run.py currently reads:
outline/taxonomy.yml, oroutline/chapter_skeleton.yml + outline/section_briefs.jsonlassets/outline_defaults.yamlThe optional style references under ref/agent-surveys/ are for human calibration only:
ref/agent-surveys/STYLE_REPORT.md to sanity-check chapter counts / thicknessref/agent-surveys/text/ only to calibrate structure rather than wordinguv run python .codex/skills/outline-builder/scripts/run.py --workspace <workspace>--workspace <dir>--unit-id <id>--inputs <path1;path2>--outputs <path1;path2>--checkpoint <C*>uv run python .codex/skills/outline-builder/scripts/run.py --workspace <workspace>Related Work still carries domain-specific framing, patch assets/outline_defaults.yaml before changing Python.references/stage_a_contract.md and references/examples_good.md.outline-budgeter rather than expanding this script.Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
Analyzes job descriptions and generates tailored resumes that highlight relevant experience, skills, and achievements to maximize interview chances
Generate Excalidraw diagrams from natural language descriptions. Use when asked to "create a diagram", "make a flowchart", "visualize a process", "draw a system architecture", "create a mind map", or "generate an Excalidraw file". Supports flowcharts, relationship diagrams, mind maps, and system architecture diagrams. Outputs .excalidraw JSON files that can be opened directly in Excalidraw.
Build and distribute Expo development clients locally or via TestFlight
Use when you have a written implementation plan to execute in a separate session with review checkpoints
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
Take willoscar/outline-builder from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.