Quarto document authoring and markdown conversion.
Author

Mickaël Canouil (@mcanouil)

Quarto Authoring

This skill is based on Quarto CLI v1.9.36, released 2026-03-19.

When to Use What

Task: Write a new Quarto document Use: Follow “QMD Essentials” below, then see specific reference files

Task: Add cross-references Use: references/cross-references.md

Task: Configure code cells Use: references/code-cells.md

Task: Add figures with captions Use: references/figures.md

Task: Create tables Use: references/tables.md

Task: Add citations and bibliography Use: references/citations.md

Task: Add callout blocks Use: references/callouts.md

Task: Add diagrams (Mermaid, Graphviz) Use: references/diagrams.md

Task: Control page layout Use: references/layout.md

Task: Use shortcodes Use: references/shortcodes.md

Task: Add conditional content Use: references/conditional-content.md

Task: Use divs and spans Use: references/divs-and-spans.md

Task: Configure YAML front matter Use: references/yaml-front-matter.md

Task: Find and use extensions Use: references/extensions.md

Task: Apply markdown linting rules Use: references/markdown-linting.md

Task: Choose or configure a compute engine (knitr, jupyter, julia) Use: references/engines.md

Migration (only when converting an existing project)

Do NOT read these references when writing new Quarto documents. Only read the one matching the source format when the user explicitly asks to convert or migrate an existing project.

QMD Essentials

Basic Document Structure

---
title: "Document Title"
author: "Author Name"
date: today
format: html
---

Content goes here.

A Quarto document consists of two main parts:

  1. YAML Front Matter: Metadata and configuration at the top, enclosed by ---.
  2. Markdown Content: Main body using standard markdown syntax.

Divs and Spans

Divs use fenced syntax with three colons:

::: {.class-name}
Content inside the div.
:::

Spans use bracketed syntax:

This is [important text]{.highlight}.

Details: references/divs-and-spans.md

Code Cell Options Syntax

A code cell starts with triple backticks and a language identifier between curly braces. Code cells are code blocks that can be executed to produce output.

Quarto uses the language’s comment symbol + | for cell options. Options use dashes, not dots (e.g., fig-cap not fig.cap).

  • R, Python, Julia: #|
  • Mermaid: %%|
  • Graphviz/DOT: //|
```{language}
#| label: fig-example
#| echo: false
#| fig-cap: "A scatter plot example."

# code that produces a figure
```

Set document-level defaults in YAML front matter:

execute:
  echo: false
  warning: false

Caching — critical engine difference: Only suggest #| cache: true for R code cells (knitr engine). Never suggest it for other language cells — it does not work and will be silently ignored. The only correct approach is execute: cache: true in the top-level YAML front matter when using engines other than knitr. Python/Jupyter requires jupyter-cache (pip install jupyter-cache):

execute:
  cache: true

Details: references/code-cells.md

Cross-References

Labels must start with a type prefix. Reference with @:

  • Figure: fig- prefix, e.g., #| label: fig-plot → @fig-plot
  • Table: tbl- prefix, e.g., #| label: tbl-data → @tbl-data
  • Section: sec- prefix, e.g., {#sec-intro} → @sec-intro
  • Equation: eq- prefix, e.g., {#eq-model} → @eq-model
```{language}
#| label: fig-plot
#| fig-cap: "A caption for the plot."

# code that produces a figure
```

See @fig-plot for the results.

Details: references/cross-references.md

Callout Blocks

Five types: note, warning, important, tip, caution.

::: {.callout-note}
This is a note callout.
:::

::: {.callout-warning}

## Custom Title

This is a warning with a custom title.

:::

Details: references/callouts.md

Figures

![Caption text](image.png){#fig-name fig-alt="Alt text"}

Subfigures:

::: {#fig-group layout-ncol=2}
![Sub caption 1](image1.png){#fig-sub1}

![Sub caption 2](image2.png){#fig-sub2}

Main caption for the group.
:::

Details: references/figures.md

Tables

::: {#tbl-example}

| Column 1 | Column 2 |
| -------- | -------- |
| Data 1   | Data 2   |

Table caption.
:::

Details: references/tables.md

Citations

According to @smith2020, the results show...
Multiple citations [@smith2020; @jones2021].

Configure in YAML:

bibliography: references.bib
csl: apa.csl

Details: references/citations.md

Common Workflows

Creating an HTML Document

title: "My Report"
author: "Your Name"
date: today
format:
  html:
    toc: true
    code-fold: true
    theme: cosmo

Creating a PDF Document

title: "My Report"
format:
  pdf:
    documentclass: article
    papersize: a4

Creating a RevealJS Presentation

---
title: "My Presentation"
format: revealjs
---

## First Slide

Content here.

## Second Slide

More content.

Setting Up a Quarto Project

Create _quarto.yml in the project root:

project:
  type: website

website:
  title: "My Site"
  navbar:
    left:
      - href: index.qmd
        text: Home
      - href: about.qmd
        text: About

format:
  html:
    theme: cosmo

Relationship to other skills

This skill covers general Quarto authoring and documents the upstream chunk-option syntax (#| label: fig-..., #| fig-cap: "...") that Quarto itself supports for figure and table captions. This repo overrides that convention for its own .qmd files: shared/writing/quarto-figure-captions.md requires div syntax (::: {#fig-...} / ::: {#tbl-...}) instead, and that lab-specific rule takes precedence over the chunk-option examples in this skill’s references/figures.md and references/tables.md whenever the document under edit belongs to this repo.

Resources

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Reuse

MIT