# Paper Workflow

> Use when deciding which paper-related skill to use or how to sequence manuscript work from project setup through submission and rebuttal.

- Skill: `chanw-research/paper-workflow` (Agent Skill)
- Install (CLI): `npx skillmds@latest add chanw-research/paper-workflow`
- Raw SKILL.md: https://api.skillmd.com/api/skills/chanw-research/paper-workflow/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Productivity
- Author: chanw-research (https://skillmd.com/u/chanw-research)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/chanw-research/paper-workflow

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# Paper Workflow

## Overview

Use this skill as the routing map for paper work. It does not replace the specialized skills. It tells you which one to use next.

Default assumption: unless the user explicitly names a conference venue, the manuscript should follow the journal-oriented, `Nature`-style workflow.

When writing follows experiments or analysis performed across multiple sessions, freeze a compact handoff first: current paper story, supported findings, unresolved decisions, and the figure list that actually carries those findings.

## Routing Map

Use:
- `paper-bootstrap` when a project is new, messy, or missing a source of truth
- `nature-portfolio-playbook` when the target is `Nature`, `Nature Methods`, `Nature Biotechnology`, or the venue fit among those journals is still unclear
- `scientific-writing` when drafting or rewriting sections in prose
- `manuscript-optimizer` when the paper's claim structure, evidence chain, terminology, or prose need revision
- `results-section-revision` when the Results section is scientifically stable but the subsection flow, paragraph openings, or argument progression still feel jumpy
- `figure-planner` when the main bottleneck is figure logic, panel roles, or legend sync
- `citation-verifier` when bibliography hygiene or source verification is the bottleneck
- `data-availability` when repository plans, accession numbers, source-data coverage, or Data Availability wording are the bottleneck
- `submission-audit` when the paper is near submission or resubmission and needs a preflight pass
- `rebuttal-response` when reviewer comments exist and a response letter plus aligned manuscript edits are needed
- `conference-paper-writing` only when the user explicitly wants a conference paper for venues such as NeurIPS, ICML, ICLR, ACL, AAAI, or COLM

## Default Sequence

For most journal manuscripts, prefer this order:

1. `paper-bootstrap`
2. `nature-portfolio-playbook` when venue fit or article type is uncertain
3. Refresh `notes/project_truth.md`, `notes/result_summary.md`, and `notes/paper_handoff.md` after any major experimental or figure update
4. `scientific-writing` or `manuscript-optimizer`
5. `figure-planner`
6. `results-section-revision` when Results is substantively right but narratively abrupt
7. `citation-verifier`
8. `data-availability`
9. `submission-audit`
10. `rebuttal-response` after external review

## Common Mistakes

- using conference-style writing skills by default for journal manuscripts
- polishing sections before the active manuscript source of truth is clear
- rewriting the manuscript from experiment memory instead of a current `result_summary.md` or `paper_handoff.md`
- editing figure legends late without rechecking the Results text
- leaving repository choice, accession IDs, or source-data coverage until the submission portal is already open
- postponing Nature Portfolio article-type or venue-fit decisions until after the paper is mostly rewritten
- treating citation formatting as the same thing as citation verification
- writing a response letter before deciding the underlying manuscript edits