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npx skills add https://github.com/WILLOSCAR/research-units-pipeline-skills --skill global-reviewer
Purpose: make the draft read like a coherent paper (not stitched subsections) and make problems auditable.
Mission: find cross-section issues a real reviewer would flag, and route them to the right upstream fix.
Do:
Avoid:
Mission: spot stitched-island structure and front-matter weaknesses that cause it.
Do:
Avoid:
You are a meticulous reviewer for a survey manuscript.
Your job is to surface cross-section problems that would matter to a real reader/reviewer:
- missing or underspecified evidence for claims
- scope drift and taxonomy inconsistency
- weak front matter (boundary/methodology not stated, so H3s carry repeated disclaimers)
- stitched-island structure (no argument chain across sections)
Constraints:
- do not invent facts or citations
- do not add new citation keys
- treat missing evidence as a failure signal: route upstream instead of writing around it
Output style:
- bullets-first
- actionable, route-to-skill recommendations
This is not “polish for style”. It is a contract check:
output/DRAFT.mdoutline/outline.ymloutline/taxonomy.ymloutline/mapping.tsvoutline/claim_evidence_matrix.mdcitations/ref.biboutput/GLOBAL_REVIEW.md (bullets-first report; always written)output/DRAFT.md (optional safe edits; only when edits are low-risk)Owns:
Does not own:
1) Check structure against outline/outline.yml
2) Check scope vocabulary against outline/taxonomy.yml
3) Check coverage signals via outline/mapping.tsv
4) Spot-check claims using outline/claim_evidence_matrix.md
5) Sanity-check citation keys against citations/ref.bib
output/GLOBAL_REVIEW.md must be bullets-first and contain these headings verbatim (so gates can verify them):
## A. Input integrity / placeholder leakage## B. Narrative and argument chain## C. Scope and taxonomy consistency## D. Citations and verifiability (claim -> evidence)## E. Tables and structural outputsInclude a top line:
- Status: PASS (or - Status: OK) only after all blocking issues are addressed.Look for:
…, TODO, “enumerate 2-4 …”, “scope/design space/evaluation practice”)Action:
Goal: every section does an argument move.
Check:
This subsection ...) and slide navigation (Next, we ...).Action (safe edits allowed):
Bad:
Next, we move from planning to memory.Better:
Planning specifies how decisions are made; memory determines what information those decisions can reliably condition on under a fixed protocol.Check:
Action:
Write a small claim-evidence table (5–10 rows):
claim | section | citations | evidence_field | evidence_levelFlag:
Action:
Check:
Action:
When the report finds issues, recommend the smallest fix path:
paper-notes → evidence-draft → anchor-sheet → writer-context-pack)writer-selfloop / subsection-polisher / draft-polisher)section-mapper / evidence-binder) then rewrite the affected sectionscitation-diversifier → citation-injector (then draft-polisher)If and only if edits are low-risk and do not change citation keys:
This skill includes a deterministic helper script that generates a gate-compliant output/GLOBAL_REVIEW.md from the current draft and context (no invented facts/citations).
uv run python .codex/skills/global-reviewer/scripts/run.py --helpuv run python .codex/skills/global-reviewer/scripts/run.py --workspace <workspace>--workspace <dir>--unit-id <U###> (optional; for logs)--inputs <semicolon-separated> (rare override; prefer defaults)--outputs <semicolon-separated> (rare override; default writes output/GLOBAL_REVIEW.md)--checkpoint <C#> (optional)uv run python .codex/skills/global-reviewer/scripts/run.py --workspace <workspace>Freeze policy:
output/GLOBAL_REVIEW.refined.ok to prevent overwrites.Notes:
Fix:
citation-verifier and ensure citations/ref.bib contains every cited key in output/DRAFT.md.Fix:
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/global-reviewer 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.