Initiate work on the website (#76)

* update the errorStrategy and messaging with tbprofiler

* add a local conda profile for conda issues on clusters

* limit cpus to iqtree

* add local envs

* Update README.md (#72)

Co-authored-by: TORCH-UAntwerpen <98338605+TORCH-UAntwerpen@users.noreply.github.com>

* refactor baseDir to projectDir

* Update selector expression

* Add further testing wrt containers and local (+ conda) envs

* Add a note for conda envs

* Initial commit for the website with default template

* Add basic sections

* Be explicit while installing conda envs

* Update conda_envs/setup_conda_envs.sh

Co-authored-by: LennertVerboven <lennert.verboven@uantwerpen.be>
Co-authored-by: TORCH-UAntwerpen <98338605+TORCH-UAntwerpen@users.noreply.github.com>

conda_envs/setup_conda_envs.sh

@@ -4,6 +4,8 @@ set -xue
 
 # NOTE: These environments must be in /path/to/xbs-nf/conda_envs folder
 
+# NOTE: If there are problems in `mamba`, replace it with `conda``
+
 mamba create -p ./xbs-nf-env-1 bioconda::gatk4=4.2.4.1 conda-forge::R=4.1  conda-forge::r-ggplot2=3.3.5 bioconda::datamash=1.1.0 bioconda::delly=0.8.7 bioconda::lofreq=2.1.5 bioconda::delly=0.8.7 bioconda::lofreq=2.1.5 bioconda::tb-profiler=4.1.1 bioconda::multiqc=1.11 bioconda::fastqc=0.11.8
 
 mamba create -p ./xbs-nf-env-2 jemunro::quanttb=1.01 bioconda::bwa=0.7.17 bioconda::samtools=1.9 bioconda::iqtree=2.1.2 bioconda::snp-dists=0.8.2 bioconda::snp-sites=2.4.0 bioconda::bcftools=1.9 bioconda::snpeff=4.3.1t bioconda::clusterpicker=1.2.3

modules/tbprofiler/load_library.nf

@@ -25,7 +25,7 @@ process TBPROFILER_LOAD_LIBRARY {
 
             """
             echo "A container ${workflow.container} is used: TRUE"
-            echo "resistanceDB status: ${resistanceDb}"
+            echo "resistanceDB status: ${resistanceDb.name}"
 
 
             echo "Do NOT load the library"

website/.gitignore

@@ -0,0 +1,20 @@
+# Dependencies
+/node_modules
+
+# Production
+/build
+
+# Generated files
+.docusaurus
+.cache-loader
+
+# Misc
+.DS_Store
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local
+
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*

website/README.md

@@ -0,0 +1,41 @@
+# Website
+
+This website is built using [Docusaurus 2](https://docusaurus.io/), a modern static website generator.
+
+### Installation
+
+```
+$ yarn
+```
+
+### Local Development
+
+```
+$ 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
+
+```
+$ yarn build
+```
+
+This command generates static content into the `build` directory and can be served using any static contents hosting service.
+
+### Deployment
+
+Using SSH:
+
+```
+$ USE_SSH=true yarn deploy
+```
+
+Not using SSH:
+
+```
+$ GIT_USER=<Your GitHub username> 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.

website/babel.config.js

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

website/blog/2019-05-28-first-blog-post.md

@@ -0,0 +1,12 @@
+---
+slug: first-blog-post
+title: First Blog Post
+authors:
+  name: Gao Wei
+  title: Docusaurus Core Team
+  url: https://github.com/wgao19
+  image_url: https://github.com/wgao19.png
+tags: [hola, docusaurus]
+---
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

website/blog/2019-05-29-long-blog-post.md

@@ -0,0 +1,44 @@
+---
+slug: long-blog-post
+title: Long Blog Post
+authors: endi
+tags: [hello, docusaurus]
+---
+
+This is the summary of a very long blog post,
+
+Use a `<!--` `truncate` `-->` comment to limit blog post size in the list view.
+
+<!--truncate-->
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

website/blog/2021-08-01-mdx-blog-post.mdx

@@ -0,0 +1,20 @@
+---
+slug: mdx-blog-post
+title: MDX Blog Post
+authors: [slorber]
+tags: [docusaurus]
+---
+
+Blog posts support [Docusaurus Markdown features](https://docusaurus.io/docs/markdown-features), such as [MDX](https://mdxjs.com/).
+
+:::tip
+
+Use the power of React to create interactive blog posts.
+
+```js
+<button onClick={() => alert('button clicked!')}>Click me!</button>
+```
+
+<button onClick={() => alert('button clicked!')}>Click me!</button>
+
+:::

website/blog/2021-08-26-welcome/index.md

@@ -0,0 +1,25 @@
+---
+slug: welcome
+title: Welcome
+authors: [slorber, yangshun]
+tags: [facebook, hello, docusaurus]
+---
+
+[Docusaurus blogging features](https://docusaurus.io/docs/blog) are powered by the [blog plugin](https://docusaurus.io/docs/api/plugins/@docusaurus/plugin-content-blog).
+
+Simply add Markdown files (or folders) to the `blog` directory.
+
+Regular blog authors can be added to `authors.yml`.
+
+The blog post date can be extracted from filenames, such as:
+
+- `2019-05-30-welcome.md`
+- `2019-05-30-welcome/index.md`
+
+A blog post folder can be convenient to co-locate blog post images:
+
+![Docusaurus Plushie](./docusaurus-plushie-banner.jpeg)
+
+The blog supports tags as well!
+
+**And if you don't want a blog**: just delete this directory, and use `blog: false` in your Docusaurus config.

website/blog/authors.yml

@@ -0,0 +1,17 @@
+endi:
+  name: Endilie Yacop Sucipto
+  title: Maintainer of Docusaurus
+  url: https://github.com/endiliey
+  image_url: https://github.com/endiliey.png
+
+yangshun:
+  name: Yangshun Tay
+  title: Front End Engineer @ Facebook
+  url: https://github.com/yangshun
+  image_url: https://github.com/yangshun.png
+
+slorber:
+  name: Sébastien Lorber
+  title: Docusaurus maintainer
+  url: https://sebastienlorber.com
+  image_url: https://github.com/slorber.png

website/docs/frequenty-asked-questions/_category_.json

@@ -0,0 +1,4 @@
+{
+  "label": "Troubleshooting",
+  "position": 3
+}

website/docs/frequenty-asked-questions/manage-docs-versions.md

@@ -0,0 +1,55 @@
+---
+sidebar_position: 1
+---
+
+# Manage Docs Versions
+
+Docusaurus can manage multiple versions of your docs.
+
+## Create a docs version
+
+Release a version 1.0 of your project:
+
+```bash
+npm run docusaurus docs:version 1.0
+```
+
+The `docs` folder is copied into `versioned_docs/version-1.0` and `versions.json` is created.
+
+Your docs now have 2 versions:
+
+- `1.0` at `http://localhost:3000/docs/` for the version 1.0 docs
+- `current` at `http://localhost:3000/docs/next/` for the **upcoming, unreleased docs**
+
+## Add a Version Dropdown
+
+To navigate seamlessly across versions, add a version dropdown.
+
+Modify the `docusaurus.config.js` file:
+
+```js title="docusaurus.config.js"
+module.exports = {
+  themeConfig: {
+    navbar: {
+      items: [
+        // highlight-start
+        {
+          type: 'docsVersionDropdown',
+        },
+        // highlight-end
+      ],
+    },
+  },
+};
+```
+
+The docs version dropdown appears in your navbar:
+
+![Docs Version Dropdown](/img/tutorial/docsVersionDropdown.png)
+
+## Update an existing version
+
+It is possible to edit versioned docs in their respective folder:
+
+- `versioned_docs/version-1.0/hello.md` updates `http://localhost:3000/docs/hello`
+- `docs/hello.md` updates `http://localhost:3000/docs/next/hello`

website/docs/frequenty-asked-questions/translate-your-site.md

@@ -0,0 +1,88 @@
+---
+sidebar_position: 2
+---
+
+# Translate your site
+
+Let's translate `docs/intro.md` to French.
+
+## Configure i18n
+
+Modify `docusaurus.config.js` to add support for the `fr` locale:
+
+```js title="docusaurus.config.js"
+module.exports = {
+  i18n: {
+    defaultLocale: 'en',
+    locales: ['en', 'fr'],
+  },
+};
+```
+
+## Translate a doc
+
+Copy the `docs/intro.md` file to the `i18n/fr` folder:
+
+```bash
+mkdir -p i18n/fr/docusaurus-plugin-content-docs/current/
+
+cp docs/intro.md i18n/fr/docusaurus-plugin-content-docs/current/intro.md
+```
+
+Translate `i18n/fr/docusaurus-plugin-content-docs/current/intro.md` in French.
+
+## Start your localized site
+
+Start your site on the French locale:
+
+```bash
+npm run start -- --locale fr
+```
+
+Your localized site is accessible at `http://localhost:3000/fr/` and the `Getting Started` page is translated.
+
+:::caution
+
+In development, you can only use one locale at a same time.
+
+:::
+
+## Add a Locale Dropdown
+
+To navigate seamlessly across languages, add a locale dropdown.
+
+Modify the `docusaurus.config.js` file:
+
+```js title="docusaurus.config.js"
+module.exports = {
+  themeConfig: {
+    navbar: {
+      items: [
+        // highlight-start
+        {
+          type: 'localeDropdown',
+        },
+        // highlight-end
+      ],
+    },
+  },
+};
+```
+
+The locale dropdown now appears in your navbar:
+
+![Locale Dropdown](/img/tutorial/localeDropdown.png)
+
+## Build your localized site
+
+Build your site for a specific locale:
+
+```bash
+npm run build -- --locale fr
+```
+
+Or build your site to include all the locales at once:
+
+```bash
+npm run build
+```