Course notes for Metagenomics Bioinformatics at MGnify (2024) course

Authoring

To edit the materials, you can just add/edit Markdown files (using normal markdown or Quarto flavoured Markdown) in the sessions/ directory.

To preview your changes, you need to install Quarto.

And run quarto preview . in this directory.

Converting older materials

If you're converting materials from RST format in earlier year's courses, you might find the following prompt helpful for your LLM of choice:

Convert the following .rst file into Quarto Markdown (.qmd).
When there is a block starting `|image2|`, turn it into a callout using `:::{.callout-step .callout-tip}`.
When there is a block starting `|image3|`, turn it into a callout using `:::{.callout-question .callout-tip}`.
For other images, put a line in saying `TODO: image`.

```
******************
My old page in rst
******************
lorem ipsum
```

Callout blocks

Quarto supports callout blocks to make certain text stand out. There are defaults like "tip", "note", "warning". We also have custom callouts for "step" and "question". They can be used like this:

# A section
This is some ordinary text.
::: {.callout-tip}
This is a tip
:::

::: {.callout-tip}
# Hint!
This is a tip with a custom title
:::

::: {.callout-step .callout-tip}
# Run MultiQC
This is a special "step" callout detailing what the participant should do next,
e.g.
```bash
run --some --code
```
:::

And finally
::: {.callout-question .callout-tip}
This is a question the participant should think about?
:::