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. 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.