This repository contains a simple Quarto template for use in nf-core HTML reports and nf-core presentations. Quarto works with both Python and R out of the box, as well as for both HTML/PDF reports and revealjs-based presentations.

If you've already installed Quarto you can install the template like so:

quarto use template fasterius/nf-core-quarto-template

This will install the template (i.e. create the _extensions/ directory in your current location) and create an example .qmd file that you can use as a starting place for your report. You can also just install the template itself without getting the .qmd file like so:

quarto add fasterius/nf-core-quarto-template

After a successful installation you can use the template by specifying e.g. the HTML format in your YAML header, like so:

...
format:
    nf-core-html: default
...

You can also use the included reveal.js format:

...
format:
    nf-core-revealjs: default
...

The template uses the nf-core colours for e.g. table of contents, inline code and syntax highlighting. You can check the default format specifications in the _extension.yml file, which can be overridden by your own YAML header, like so:

...
format:
    nf-core-html:
        embed-resources: false
        highlight-style: arrow
...

You can find a minimal example in the template.qmd file. While the example is using R and the knitr engine you can easily use a Jupyter kernel instead by specifying e.g. jupyter: python3.