refactor: Init with Docusaurus

npx @docusaurus/init@latest init my-website classic

.gitignore

@@ -1,12 +1,20 @@
-pids
-logs
-node_modules
-npm-debug.log
-coverage/
-run
-dist
+# Dependencies
+/node_modules
+
+# Production
+/build
+
+# Generated files
+.docusaurus
+.cache-loader
+
+# Misc
 .DS_Store
-.nyc_output
-.basement
-config.local.js
-basement_dist
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local
+
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*

README.md

@@ -1,3 +1,33 @@
-NXF_VER=20.11.0-edge nextflow run nf-core/chipseq -r 1.2.1 -profile utd_ganymede -params-file nf-params.json
+# Website
 
-Turn this into a [Learning Lab](https://lab.github.com/new)
+This website is built using [Docusaurus 2](https://docusaurus.io/), a modern static website generator.
+
+## Installation
+
+```console
+yarn install
+```
+
+## Local Development
+
+```console
+yarn start
+```
+
+This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.
+
+## Build
+
+```console
+yarn build
+```
+
+This command generates static content into the `build` directory and can be served using any static contents hosting service.
+
+## Deployment
+
+```console
+GIT_USER=<Your GitHub username> USE_SSH=true yarn deploy
+```
+
+If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the `gh-pages` branch.

babel.config.js

@@ -0,0 +1,3 @@
+module.exports = {
+  presets: [require.resolve('@docusaurus/core/lib/babel/preset')],
+};

docs/intro.md

@@ -0,0 +1,35 @@
+---
+sidebar_position: 1
+---
+
+# Tutorial Intro
+
+Let's discover **Docusaurus in less than 5 minutes**.
+
+## Getting Started
+
+Get started by **creating a new site**.
+
+Or **try Docusaurus immediately** with **[new.docusaurus.io](https://new.docusaurus.io)**.
+
+## Generate a new site
+
+Generate a new Docusaurus site using the **classic template**:
+
+```shell
+npx @docusaurus/init@latest init my-website classic
+```
+
+## Start your site
+
+Run the development server:
+
+```shell
+cd my-website
+
+npx docusaurus start
+```
+
+Your site starts at `http://localhost:3000`.
+
+Open `docs/intro.md` and edit some lines: the site **reloads automatically** and display your changes.

docs/tutorial-basics/_category_.json

@@ -0,0 +1,4 @@
+{
+  "label": "Tutorial - Basics",
+  "position": 2
+}

docs/tutorial-basics/congratulations.md

@@ -0,0 +1,21 @@
+---
+sidebar_position: 6
+---
+
+# Congratulations!
+
+You have just learned the **basics of Docusaurus** and made some changes to the **initial template**.
+
+Docusaurus has **much more to offer**!
+
+Have **5 more minutes**? Take a look at **[versioning](../tutorial-extras/manage-docs-versions.md)** and **[i18n](../tutorial-extras/translate-your-site.md)**.
+
+Anything **unclear** or **buggy** in this tutorial? [Please report it!](https://github.com/facebook/docusaurus/discussions/4610)
+
+## What's next?
+
+- Read the [official documentation](https://docusaurus.io/).
+- Add a custom [Design and Layout](https://docusaurus.io/docs/styling-layout)
+- Add a [search bar](https://docusaurus.io/docs/search)
+- Find inspirations in the [Docusaurus showcase](https://docusaurus.io/showcase)
+- Get involved in the [Docusaurus Community](https://docusaurus.io/community/support)

docs/tutorial-basics/create-a-blog-post.md

@@ -0,0 +1,29 @@
+---
+sidebar_position: 3
+---
+
+# Create a Blog Post
+
+Docusaurus creates a **page for each blog post**, but also a **blog index page**, a **tag system**, an **RSS** feed...
+
+## Create your first Post
+
+Create a file at `blog/2021-02-28-greetings.md`:
+
+```md title="blog/2021-02-28-greetings.md"
+---
+slug: greetings
+title: Greetings!
+author: Steven Hansel
+author_title: Docusaurus Contributor
+author_url: https://github.com/ShinteiMai
+author_image_url: https://github.com/ShinteiMai.png
+tags: [greetings]
+---
+
+Congratulations, you have made your first post!
+
+Feel free to play around and edit this post as much you like.
+```
+
+A new blog post is now available at `http://localhost:3000/blog/greetings`.

docs/tutorial-basics/create-a-document.md

@@ -0,0 +1,56 @@
+---
+sidebar_position: 2
+---
+
+# Create a Document
+
+Documents are **groups of pages** connected through:
+
+- a **sidebar**
+- **previous/next navigation**
+- **versioning**
+
+## Create your first Doc
+
+Create a markdown file at `docs/hello.md`:
+
+```md title="docs/hello.md"
+# Hello
+
+This is my **first Docusaurus document**!
+```
+
+A new document is now available at `http://localhost:3000/docs/hello`.
+
+## Configure the Sidebar
+
+Docusaurus automatically **creates a sidebar** from the `docs` folder.
+
+Add metadatas to customize the sidebar label and position:
+
+```diff title="docs/hello.md"
++ ---
++ sidebar_label: "Hi!"
++ sidebar_position: 3
++ ---
+
+
+# Hello
+
+This is my **first Docusaurus document**!
+```
+
+It is also possible to create your sidebar explicitly in `sidebars.js`:
+
+```diff title="sidebars.js"
+module.exports = {
+  tutorialSidebar: [
+    {
+      type: 'category',
+      label: 'Tutorial',
+-     items: [...],
++     items: ['hello'],
+    },
+  ],
+};
+```

docs/tutorial-basics/create-a-page.md

@@ -0,0 +1,43 @@
+---
+sidebar_position: 1
+---
+
+# Create a Page
+
+Add **Markdown or React** files to `src/pages` to create a **standalone page**:
+
+- `src/pages/index.js` -> `localhost:3000/`
+- `src/pages/foo.md` -> `localhost:3000/foo`
+- `src/pages/foo/bar.js` -> `localhost:3000/foo/bar`
+
+## Create your first React Page
+
+Create a file at `src/pages/my-react-page.js`:
+
+```jsx title="src/pages/my-react-page.js"
+import React from 'react';
+import Layout from '@theme/Layout';
+
+export default function MyReactPage() {
+  return (
+    <Layout>
+      <h1>My React page</h1>
+      <p>This is a React page</p>
+    </Layout>
+  );
+}
+```
+
+A new page is now available at `http://localhost:3000/my-react-page`.
+
+## Create your first Markdown Page
+
+Create a file at `src/pages/my-markdown-page.md`:
+
+```mdx title="src/pages/my-markdown-page.md"
+# My Markdown page
+
+This is a Markdown page
+```
+
+A new page is now available at `http://localhost:3000/my-markdown-page`.

docs/tutorial-basics/deploy-your-site.md

@@ -0,0 +1,31 @@
+---
+sidebar_position: 5
+---
+
+# Deploy your site
+
+Docusaurus is a **static-site-generator** (also called **[Jamstack](https://jamstack.org/)**).
+
+It builds your site as simple **static HTML, JavaScript and CSS files**.
+
+## Build your site
+
+Build your site **for production**:
+
+```bash
+npm run build
+```
+
+The static files are generated in the `build` folder.
+
+## Deploy your site
+
+Test your production build locally:
+
+```bash
+npm run serve
+```
+
+The `build` folder is now served at `http://localhost:3000/`.
+
+You can now deploy the `build` folder **almost anywhere** easily, **for free** or very small cost (read the **[Deployment Guide](https://docusaurus.io/docs/deployment)**).