nature-writing

The full skill.

Original instructions from the publisher’s SKILL.md

# Nature-Style Scientific Writing — Router

## Routing protocol

For a new drafting task, follow the routing below. For follow-up edits, reuse established task choices and already loaded guidance; read additional fragments only when the requested scope changes.

### 1. Load the manifest and the core layer

Read [manifest.yaml](manifest.yaml). It declares the axes (`task`, `paper_type`, `section`, `language`, `journal`), the allowed values, and the file paths each value maps to.

Also read every file listed under `always_load`. These hold the default stance, writing workflow, and output format that apply to every drafting job.

### 2. Detect the axis values for this request

For each axis in the manifest, decide the value using the manifest's `detect:` hint and the user's input:

- `task` — manuscript / submission-package. Use `submission-package` for first-submission materials, never for revision correspondence.
- `paper_type` — research / methods / hypothesis / algorithmic / review. Default: research.
- `section` — abstract / intro / related-work / method / experiments / discussion / conclusion / title. May be multiple. Ask the user if it is ambiguous and matters for the draft.
- `language` — en or zh-to-en. Detect from the user's notes themselves.
- `journal` — nature / nature-family / nat-comms / nat-mach-intell / generic.
  Default: generic. Use `nature` only for the flagship journal Nature,
  `nat-comms` for Nature Communications, `nat-mach-intell` for Nature Machine
  Intelligence (NMI), and `nature-family` for other Nature Portfolio titles or
  an unspecified Nature-family request.

State the detected axis values in one short line to the user before drafting, so they can correct you cheaply. This is a progress update, not an approval gate; continue unless a necessary decision remains unresolved.

### 3. Load the matching fragments

For each axis value, Read the file mapped in the manifest. Skip the `section` axis when the task is `submission-package` or when the user explicitly asks for a free-floating argument paragraph with no section context.

Do **not** read every fragment in `static/`. Load only what step 2 selected.

### 4. Draft using the loaded material

Apply the loaded fragments in this priority order:

1. Core stance + intake (`core/stance.md`) — surface missing claim / evidence / boundary before drafting.
2. Paper-type playbook — argument chain, drafting order.
3. Section-specific drafting rules and structure.
4. Task-specific submission rules when `task=submission-package`.
5. Journal-specific framing and constraints.
6. Language-specific sentence and paragraph rules (apply last).

For `task=manuscript`, use `core/workflow.md` at the requested scale. Plan the argument for a new section or substantial restructuring; a title, single paragraph, or local follow-up needs only the applicable evidence, wording, and consistency checks. Complete the requested prose unless a material unresolved decision blocks it or the user requested an outline for approval first.

When drafting or restructuring Results, or compressing a full manuscript's main
text, also load `../nature-shared/core/main-text-discipline.md` before building
the paragraph map. Classify every result by function, allocate it across main
text, captions, Methods/source data, and SI, then draft the shortest sufficient
evidence chain. Do not equate a complete analysis record with a complete main
text.

When the target is flagship Nature, Nature Communications, Nature Machine
Intelligence, or another Nature Portfolio title, load the matching shared
Nature-style corpus guidance for the section being drafted:

- Results or Discussion →
  `../nature-shared/core/nature-results-discussion.md`
- Introduction or whole-manuscript narrative →
  `../nature-shared/core/nature-introduction.md`
- Abstract → `../nature-shared/core/nature-abstract.md`

Use these files for claim escalation, question-chain alignment,
discovery-centred compression, and synthesis. They were initially distilled
from published NMI papers and generalized as Nature-style defaults; do not
present them as official policy, and let the target journal's current rules
override them.

For any Discussion drafting, restructuring, or section audit, also load
`../nature-shared/core/discussion-argument-language.md`. Use it to select the
opening anchor, control the reverse-funnel expansion, distinguish literature
positioning from citation decoration, calibrate modal strength to evidence,
and turn limitations and future work into claim-specific reasoning. This is
general writing guidance rather than an official journal rule.

For `task=submission-package`, follow `static/fragments/task/submission-package.md` and `references/submission-package.md` instead. Build the deliverable matrix and readiness audit; do not force manuscript paragraph architecture onto administrative submission materials.

If essential evidence or boundary is missing, write a placeholder and list it under `Assumptions or missing inputs:` instead of inventing content.

### 5. Reach for references only when needed

The files under `references/` are deep references and the example library, not defaults. Open them on demand per the `references.on_demand` table in the manifest. Typical triggers:

- The user asks for a concrete example or template → `references/examples/index.md`.
- A section's draft has structural problems that the section fragment alone does not explain → the matching `references/<section>.md`.
- The user needs a broad-audience `Nature` abstract opening or asks about a `summary paragraph` → `references/nature-summary-paragraph.md`.
- The user asks "does this paragraph flow?" → `references/paragraph-flow.md`.
- The user asks for a self-review or rejection-risk audit → `references/paper-review.md`.
- The user asks what belongs in the main text, captions, or SI; wants a shorter
  Results section; or is adding reviewer-driven explanation →
  `../nature-shared/core/main-text-discipline.md`.
- The user requests a complete first-submission package, templates, or a submission-readiness audit → `references/submission-package.md`.
- The target is the flagship journal Nature and exact submission or formatting
  requirements matter → `../nature-shared/journal-formats/nature.md`.
- The target is Nature Machine Intelligence and exact content-type, submission,
  data/code or production requirements matter →
  `../nature-shared/journal-formats/nature-machine-intelligence.md`.
- Any Nature / Nature Portfolio target needs Results claim progression,
  evidence-bound interpretation, robustness placement, or Discussion synthesis
  → `../nature-shared/core/nature-results-discussion.md`.
- Any target needs a Discussion function chain, evidence-calibrated modal
  language, claim-specific limitations, non-redundant literature positioning,
  or uncertainty-driven future work →
  `../nature-shared/core/discussion-argument-language.md`.
- Any Nature / Nature Portfolio target needs an Introduction funnel, exact gap,
  literature logic, question-first novelty, study roadmap, or alignment with
  Results → `../nature-shared/core/nature-introduction.md`.
- Any Nature / Nature Portfolio target needs abstract evidence-chain,
  main/supporting-claim, numeric-result, or final-payoff decisions →
  `../nature-shared/core/nature-abstract.md`.
- The work involves regulated or specialist research compliance →
  `../nature-shared/core/research-compliance.md`.

## Submission boundary

- `nature-writing` owns **initial submission** materials prepared before peer review.
- `nature-response` owns revision cover letters, rebuttals, point-by-point responses, marked manuscripts, appeals, and other post-decision correspondence.
- Route graphical abstracts and TOC graphics to `nature-figure`; route simulated pre-submission peer review to `nature-reviewer`.