paper-workflow

Name: paper-workflow
Author: Boom5426/Nature-Paper-Skills

$npx mdskill add Boom5426/Nature-Paper-Skills/paper-workflow

Route paper tasks to specialized skills for seamless workflow.

Selects the optimal paper-related skill based on project stage and goals.
Depends on user input regarding conference venues or journal targets.
Analyzes project state to recommend the next appropriate action.
Outputs clear routing instructions for executing specific paper tasks.

SKILL.md

.github/skills/paper-workflowView on GitHub ↗

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

# 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

More from Boom5426/Nature-Paper-Skills

Skill	Description
academic-presentations	>-
academic-researcher	Use when conducting literature reviews, summarizing papers, comparing methodologies, identifying research gaps, or supporting scholarly writing across disciplines.
citation-verifier	Use when checking manuscript citations, bibliography hygiene, DOI or PMID completeness, placeholder references, or BibTeX consistency before submission or revision.
conference-paper-writing	Use when writing or revising ML or AI conference papers for venues such as NeurIPS, ICML, ICLR, ACL, AAAI, or COLM, especially when the workflow is conference-first rather than Nature-style journal-first.
data-availability	Use when drafting, auditing, or revising Data Availability statements, repository plans, accession-number placement, source-data coverage, or restricted-data wording for journal submission or resubmission.
figure-planner	Use when designing, restructuring, or auditing manuscript figures and you need to define one main claim per figure, assign panel roles, align legends with the text, or decide what belongs in main figures versus supplement.
manuscript-optimizer	Use when reviewing or revising an academic manuscript whose central claim, evidence chain, figures, terminology, and prose may have drifted out of sync before submission or resubmission.
nature-portfolio-playbook	Use when choosing among Nature, Nature Methods, or Nature Biotechnology, or when preparing a Nature Portfolio life-science manuscript for venue fit, article-type framing, and policy-aware pre-submission checks.
paper-analyzer	Use when deeply analyzing a single paper and producing structured notes on claims, methods, figures, evaluation, strengths, limitations, and related work.
paper-bootstrap	Use when starting a new manuscript project or cleaning up an existing paper directory and you need a standard structure, active source files, project memory, and venue defaults before deeper writing begins.