index.Rmd

--- 
title: "CBW Bookdown Guide"
author: "Julia Qiu, Nia Hughes"
date: "Last Updated: `r Sys.Date()`"
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib, packages.bib]
url: https://cbw-dev.github.io/bookdown-guide/ 
cover-image: img/bioinformatics_logo.png
description: |
  Guide to using the CBW Bookdown template
link-citations: yes
github-repo: cbw-dev/bookdown-guide
favicon: img/favicon.ico
---

# (PART) Introduction {-}

# CBW's Bookdown Documentation

Welcome to CBW's documentation for creating a workshop website using Bookdown. Bookdown is an R package that is used to build books, and in our case, the websites hosting CBW's workshops! You will only need to know markdown and whatever coding language you will be using to learn bookdown.

Please note: this is the documentation to create a workshop using *bookdown*. If **Jupyter Book** suits you better, see [here](https://cbw-dev.github.io/jupyterbook-docs/).

If you don't know which one to use, use the following flowchart to help decide:

<img src="https://docs.google.com/drawings/d/e/2PACX-1vT6nhnL2deZ_iW9yjfjMkyFu7S6rA4dCP0lk6bBI5bC7_fuASKa6Znf40DeIPA_47i-AltXUrtG1Zpt/pub?w=1663&amp;h=1044">

# How Bookdown Works: A Primer
Here is a general summary of how Bookdown creates html websites from .Rmd files when you hit Build.

<img src="https://docs.google.com/drawings/d/e/2PACX-1vQNLBySqW7Z1YC-a35s0rJo4V4ZAn6WumpGKxngB5Md6pW97MC3ERqkiuSw-rrdmn423YXlXPkVky8I/pub?w=792&amp;h=147">

**Knitr renders and runs all the code**, and the outputs are converted into markdown. After knitr, we  have a bunch of markdown files. **Pandoc translates this markdown into HTML**, so that we get a website! It can be helpful to know when and how these packages work to help debug later on. 

:::: {.callout type="blue" style="subtle" title="Note!"}

The Build step is *required* for changes to be reflected on the website. If you push an update and the site looks the same, you probably forgot to build.

::::


:::: {.callout type="yellow" style="important" title="For more information:"}

For more information, take a look at the [Bookdown Crash Course section.](#bookdown-crash-course)

::::