Try out Quarto

Quarto

Quarto is the successor to R-markdown. Drawing heavily from tools like Pandoc, it not only supports R but also allows the inclusion and execution of Python code, even through a Jupyter interface. To dive deeper into Quarto, visit Quarto’s official website.

I tried many other tools to create documents/websites:

  • R-markdown
  • Manubot
  • Latex
  • Markdown combined with Pandoc
  • And now Quarto

Out of these, Quarto consistently delivers the most robust output. While it’s a given that you can generate HTML documents, I was pleasantly surprised by the quality of its Word outputs. With Quarto, you can designate a template and produce a Word document tailored to your company’s specific fonts and formats.

Ever grappled with placing two images side by side in Word? Or adding referenceable legends to them? With Quarto, this task is a breeze. Moreover, you can link to or even create figures directly within the document, eliminating the copying and pasting updated image versions into a draft.

I’m particularly fond of the cite-doi option, which is facilitated by the lua filter doi2cite.lua. With this, you can just specify a DOI, and it’s seamlessly integrated into both the bibliography and the main text.

Quarto and Hugo

To use Quarto for blog post I want it to render as markdowns that can be used by hugo / wowchemy. Following the online tutorials I achived this quickly. Take the source for this post as an example.

You can either render the quarto documents localy and include the output markdown in your web page. Howevr, as others pointed out, it is easy to forget to render the quarto documents after making a change.

Because for blog posts I will mainly use the markdown features and not running code, I decided to render the quarto documents trough Github Actions.

I’ve added two rules to my GitHub Actions, to render quarto documents before building the webpage with Hugo. Now everithing is automated.

If you want to do this you will need to install all R or Python dependencies in your CI environment. See here for more infomration.

Silas Kieser
Silas Kieser
Metagenome researcher

Husband, Father & Metagenome researcher