First commit

.gitignore

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+/.quarto/
+**/.DS_Store
+**/.Rhistory
+*.code-workspace
+**/.ipynb_checkpoints
+/.luarc.json
+**/*_cache/
+**/__pycache__
+slides/**/*_files
+labs/**/*_files
+**/*.fq

404.md

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+---
+pagetitle: "404: Page not found"
+subtitle: ""
+date: ""
+toc: false
+sidebar: false
+number-sections: false
+format: html
+execute:
+  freeze: false
+---
+
+::: {style="text-align: center;"}
+
+![](assets/images/404.png)
+
+# 404: Page not found
+
+It seems like you have stumbled upon a page that doesn't exist.  
+Please check your URL again.
+
+:::

README.md

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+# Raukr 2024 • Workshop Website  
+**NBIS Summer School • Advanced R for Bioinformatics**
+
+## Environment
+
+To edit, preview and render documents, you need one or more of the following requirements:
+
+- You must use [Quarto\>=1.4.5](https://quarto.org/docs/download/)
+- If using RStudio, use [v2023.12.0 or newer](https://posit.co/download/rstudio-desktop/)
+- [VSCode](https://arinbasu.medium.com/why-quarto-with-vscode-is-a-great-data-science-tool-f0a259d28702) is a good alternative to RStudio for quarto documents
+- You need to install the R packages necessary for your topic/document
+
+:bangbang: Be wary of using the visual editor! It may mess up the code formatting.
+
+### Docker
+
+A docker container is available for rendering quarto documents and to run RStudio server.
+
+```
+docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-raukr:latest
+```
+
+**Render qmd**
+
+```
+docker run --platform=linux/amd64 --rm -u 1000:1000 -v ${PWD}:/home/rstudio/raukr ghcr.io/nbisweden/workshop-raukr:latest quarto render index.qmd
+```
+
+**Run RStudio server**
+
+```
+docker run --platform=linux/amd64 --rm -e PASSWORD=raukr -p 8787:8787 -v ${PWD}:/home/rstudio/raukr ghcr.io/nbisweden/workshop-raukr:latest
+```
+
+In browser, go to [http://localhost:8787/](http://localhost:8787/). Use following credentials:
+
+> username: rstudio
+> password: raukr
+
+## Adding/Modifying topics
+
+- Fork the repository and clone locally and create a branch
+- Keep the topic name simple, preferably one word
+- To add a **topic**, create
+  - **slides/topic/index.qmd**
+  - **labs/topic/index.qmd**
+  - The YAML metadata should minimally look like this:
+
+    ```         
+    ---
+    title: "Topic"
+    author: "Author"
+    description: "This topic covers this and that."
+    format: html
+    ---
+    ```
+
+- `format` must be `html` for reports and `revealjs` for presentations
+- For assets relating to the document (figures, files etc), create an **assets** folder
+  - **slides/topic/assets/**
+  - **labs/topic/assets/**
+
+:bulb: The document can be live previewed to view changes. Preview is automatically updated on saving the document. Sometimes, the preview can look a bit wonky, in which case, cancel and rerun.
+
+- To preview, run in terminal
+  - `quarto preview slides/topic/index.qmd`
+  - `quarto preview labs/topic/index.qmd`
+  - Saving the file updates the preview
+
+:bulb: The document is rendered to the specified output format in the output directory.
+
+- To render, run in terminal
+  - `quarto render slides/topic/index.qmd`
+  - `quarto render labs/topic/index.qmd`
+  - Rendered files are written to **/docs**
+  - To view in browser, open
+    - **docs/slides/topic/index.html**
+    - **docs/labs/topic/index.html**
+    
+:bangbang: Do not run `quarto render` as it will remove everything from **docs/** and attempt to render all the files. This might overwrite someone else's materials and also break since you won't have their R packages installed. So, only render your files.
+
+- Finally commit changes (both source files and rendered files)
+
+```
+git stage .
+git commit -m "Added topic"
+```
+
+- Push changes to your fork and send a pull request
+
+## Tips & Conventions
+
+- For compute heavy steps, save intermediates and read them in
+- Be mindful of the size of files
+  - Store large data files elsewhere (dropbox, google drive etc) and link them
+  - If you have images that are more than a few hundred KB in size, scale them down to about 600px-800px and [compress](https://compressjpeg.com/) them
+- Use simple topic labels and do not make them needlessly complex
+- The qmd files must be in the correct location when rendering/previewing else metadata from config is not used. 
+- Declare R packages at the beginning of every qmd document
+- qmd files must have a format defined, either **format: html** or **format: revealjs**
+- Make a note of the default **execute** settings in `_quarto.yml`. This applies to all documents. You can override this by copying the code below to the yaml part of your document and modifying it.
+
+  ```
+  execute:
+    eval: true
+    echo: false
+  ```
+  
+- Use level 2 heading (##) as the highest level heading
+- Bullet points are defined by `-`
+- Define options in code chunks using `#|` like `#| echo: true`
+- Adjusting dimension of images `![Caption](path/to/image.jpg){width="50%"}`
+- Divs are defined using `:::` and classes are defined using `{.class}`
+  - Example of a class on a div
+  
+  ```
+  ::: {.callout-note}
+  content
+  :::
+  ```
+- Example of a class on a span `[Content]{.class}`
+- Columns are defined as such
+
+```
+:::: {.columns}
+::: {.column width="50%"}
+Contents
+:::
+::: {.column width="50%"}
+Contents
+:::
+::::
+```
+
+- Remember to spell-check your document
+  - Language used is en-us
+
+- To view a demo report, click [here](https://nbisweden.github.io/raukr-2024/labs/demo/)
+
+### RevealJS
+
+These are slide specific info. Comparisons here are to xaringan used previously for RaukR.
+
+- Slides are defined by `##` rather than `---`
+- Manual increment is defined by `. . .` rather than `--`
+- Horizontal rule is defined by `---` rather than `***`
+- Presenter notes are defined by `:::{.notes} content :::` rather than `???`
+- For small notes in the bottom of the slide, you can use
+
+```
+::: {.aside}
+Contents
+:::
+```
+
+- If content overflows the slide in vertical direction, add class `.scrollable`
+
+```
+::: scrollable
+content
+:::
+```
+
+- To view a demo presentation, click [here](https://nbisweden.github.io/raukr-2024/slides/demo/) 

_extensions/quarto-ext/fontawesome/_extension.yml

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+title: Font Awesome support
+author: Carlos Scheidegger
+version: 1.1.0
+quarto-required: ">=1.2.269"
+contributes:
+  shortcodes:
+    - fontawesome.lua