agri-pipeline

Master orchestrator for the whole agricultural research-to-publication workflow, run as a senior agricultural scientist. Coordinates the agri skills — journal selection, research (agri-research or agri-deep-research), writing and analysis (agri-paper), figures (food-figure), peer review (agri-review), revision and finalization — into one governed path with quality gates. Same machinery as food-pipeline, grounded in agriculture and multidisciplinary literature (Q1/Q2 preferred, Q4 avoided). Use when the user wants the entire agricultural process managed end to end. Triggers: run the full agricultural paper workflow, take my field trial from research to submission, manage my whole agronomy project, agricultural research to publication, end-to-end agriculture paper.

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Repository: PangenomeAI/academic-skills-food-nutrition
Last source activity: July 17, 2026 at 01:49
Detected SKILL.md language: English
Stars: 32
Forks: 3

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name: agri-pipeline
description: Master orchestrator for the whole agricultural research-to-publication workflow, run as a senior agricultural scientist. Coordinates the agri skills — journal selection, research (agri-research or agri-deep-research), writing and analysis (agri-paper), figures (food-figure), peer review (agri-review), revision and finalization — into one governed path with quality gates. Same machinery as food-pipeline, grounded in agriculture and multidisciplinary literature (Q1/Q2 preferred, Q4 avoided). Use when the user wants the entire agricultural process managed end to end. Triggers: run the full agricultural paper workflow, take my field trial from research to submission, manage my whole agronomy project, agricultural research to publication, end-to-end agriculture paper.
metadata: {"version":"1.0.0","verified":"2026-07","delegates_to":"food-pipeline","related_skills":["agri-research","agri-deep-research","agri-paper","agri-review","food-figure","journal-selector","food-pipeline"],"references":["../agri-research/references/agriculture-domain.md"]}

# Agri-Pipeline — Research-to-Publication for Agricultural Science **Run the `food-pipeline` skill exactly** — its subagents (`intake_router`, `quality_gate`), its **stages 0–6**, its quality gates, its mode advisor, and its review/revision authorization defaults — with the agriculture substitutions in [`agri-research/references/agriculture-domain.md`](../agri-research/references/agriculture-domain.md). Read that file first. No new machinery here. ## The substitutions 1. **Persona** — a **senior agricultural scientist of the specific discipline**, carried into every stage and every skill it dispatches (domain §2). 2. **Route to the `agri-*` skills**, not the food ones: | Stage | Skill | |---|---| | 0 · ROUTE | `intake_router` + `journal-selector` (agriculture coverage map) | | 1 · RESEARCH | **`agri-research`** (or **`agri-deep-research`**) | | 2 · WRITE | **`agri-paper`** → figures via **`food-figure`** (domain-neutral) | | 3 · REVIEW | **`agri-review`** | | 4 · REVISE | **`agri-paper`** (revise) | | 5 · RE-REVIEW | **`agri-review`** (re-review) | | 6 · FINALIZE | **`agri-paper`** (format-convert) | 3. **Evidence base** — Tier 1 Q1/Q2 agriculture + Nature/Science/Cell/PNAS + Q1/Q2 adjacent disciplines; Q3 for gaps; **Q4 avoided** (domain §3). `food-figure` is used directly and deliberately — it is domain-neutral and already renders at the journal spec. ## Inherited unchanged (not optional) - **Journal resolved once** at ROUTE via `journal-selector` and passed to every downstream skill, so none re-asks. - **Knowledge reuse:** when Stage 1 runs, its evidence base is carried into Stages 3/5 so `agri-review` does **not** re-search the field — it reuses it and tops up with `agri-research` **quick brief** key reviews read in full. - **Review/revision defaults:** **one** review→revise round; a second round **and** in-place Tracked Changes on the original Word file each require **explicit author authorization**. - **Deliverables — exactly two files, both `.docx`:** one **manuscript**, and **one `Review_and_Response_Report_<slug>_<date>.docx`** carrying **both the reviewer feedback and the editing response** — `agri-review` writes the feedback at Stage 3, `agri-paper` fills each `Response (type)` into that **same file** at Stage 4, and an authorized round 2 appends `R2-*` items to it. **No separate reviewer report, no standalone response letter, never Markdown** (`food-review/references/report-format.md`). - Quality gates, anti-fabrication grounding, four-gate citations, privacy scan, `human-writing.md`, and the **mandatory AI-use disclosure**. ## Agricultural gates (domain §5) At the Stage-2 gate, do not pass a manuscript that omits **the experimental unit**, field-trial reporting (site, season/years, soil, cultivar, design, replication), or ethics/**ARRIVE** for animal work — these are the flaws that end agricultural papers at review.

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food-ppt

Turn a food & nutrition review report, evidence brief, or manuscript into a fully EDITABLE PowerPoint (.pptx) that opens in PowerPoint / Keynote / Google Slides with every title, bullet, table, and figure as a native editable object — nothing flattened to an image. Converts the outputs of food-research, food-deep-research, food-paper, and food-pipeline (or any Word/PDF/Markdown/txt source) into a well-designed deck: it plans the outline, writes concise grounded slide text with presenter notes on every slide, places figures as movable picture objects, builds the .pptx via python-pptx, and QA-checks editability. Design informed by taste-skill. Use to make slides, a presentation, a PPT, or a deck from a report or paper. Triggers: make a PPT, create slides, presentation from my report, turn this review into slides, build a deck, PPTX from my paper, journal-club slides, conference presentation.

2026-08-11

agri-ppt

Turn an agricultural-science review report, evidence brief, or manuscript into a fully EDITABLE PowerPoint (.pptx) — every title, bullet, table, and figure a native editable object, nothing flattened to an image. Same machinery as food-ppt, but for agricultural work: converts the outputs of agri-research, agri-deep-research, agri-paper, and agri-pipeline (or any Word/PDF/Markdown/txt source) into a well-designed, grounded slide deck with presenter notes on every slide. Never invents content beyond the source. Use to make slides, a presentation, a PPT, or a deck from an agricultural report or paper. Triggers: make a PPT for my agronomy paper, slides from my soil science review, presentation from my field-trial report, agricultural journal-club slides, build a deck from my crop research.

2026-08-09

food-proposal

Master orchestrator for preparing research proposals and funding-application proposals in food, nutrition & agricultural science. Like food-pipeline, but for proposals: it resolves the target funding scheme's format first (headings, order, page/word limit, font, assessment criteria), then drafts from scratch (food-deep-research for the knowledge base, food-paper to write, food-review to review) or revises an existing draft after first understanding the field. Enforces the scheme's length limit and required headings and aligns content to the assessment criteria. Built-in schemes: ARC Discovery EOI, ARC Discovery Full Application, and the UoM Ag & Food project proposal; if a scheme isn't included it asks the user to upload the guideline and extracts the format. Triggers: write a grant proposal, ARC Discovery application, funding application, research proposal, project proposal, revise my grant, prepare an EOI.

2026-08-09

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agri-pipeline

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