Hello Nextflow: Embed videos (#555)

ewels · web-flow · commit e0954561a48e · 2025-03-08T20:00:31.000-05:00
- Hello Nextflow: Add embedded walkthrough videos

- Cosmetic improvements:
    * Different icons for different training courses
    * Homepage icons: Nextflow green
    * Add pymdownx.blocks.caption for block figcaptions

- Freshen up announcement bar:
    * Add announcement for Nextflow training week
diff --git a/docs/assets/overrides/main.html b/docs/assets/overrides/main.html
@@ -1,20 +1,13 @@
 {% extends "base.html" %} {% block announce %}
 <div style="text-align: center">
-  <span>Next community training</span>:
-  <strong>{{ config.extra.announcement.date_text }}</strong> on YouTube, with
-  support on Slack
-  <span class="twemoji" style="margin-left: 0.5em">
-    {% include ".icons/fontawesome/brands/youtube.svg" %}
-  </span>
-  <span class="twemoji" style="margin-right: 0.5em">
-    {% include ".icons/fontawesome/brands/slack.svg" %}
-  </span>
+  {{ config.extra.announcement.text }}
+  <strong>{{ config.extra.announcement.text_bold }}</strong>
   <a
     class="md-button"
-    href="{{ config.extra.announcement.register_url }}"
+    href="{{ config.extra.announcement.url }}"
     target="_blank"
   >
-    Register here
+    {{ config.extra.announcement.url_text }}
     <span class="twemoji"
       ><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24">
         <path
diff --git a/docs/assets/stylesheets/extra.css b/docs/assets/stylesheets/extra.css
@@ -3,7 +3,7 @@
 [data-md-color-scheme="slate"] {
   --md-primary-fg-color: #58bd9f;
   --md-primary-fg-color--light: #c3ead3;
-  --md-primary-fg-color--dark: #1a7540;
+  --md-primary-fg-color--dark: #087f68;
   --md-admonition-icon--exercise: url('data:image/svg+xml;charset=utf-8,<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M13 18h-2v-2h2v2m0-3h-2c0-3.25 3-3 3-5 0-1.1-.9-2-2-2s-2 .9-2 2H8c0-2.21 1.79-4 4-4s4 1.79 4 4c0 2.5-3 2.75-3 5m9-3c0 5.18-3.95 9.45-9 9.95v-2.01c3.95-.49 7-3.86 7-7.94s-3.05-7.45-7-7.94V2.05c5.05.5 9 4.77 9 9.95M11 2.05v2.01c-1.46.18-2.8.76-3.91 1.62L5.67 4.26C7.15 3.05 9 2.25 11 2.05M4.06 11H2.05c.2-2 1-3.85 2.21-5.33L5.68 7.1A7.902 7.902 0 0 0 4.06 11M11 19.94v2.01c-2-.2-3.85-.99-5.33-2.21l1.42-1.42c1.11.86 2.45 1.44 3.91 1.62M2.05 13h2.01c.18 1.46.76 2.8 1.62 3.91l-1.42 1.42A10.013 10.013 0 0 1 2.05 13Z"></path></svg>');
   --md-admonition-icon--result: url('data:image/svg+xml;charset=utf-8,<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M18.5 2h-13C3.6 2 2 3.6 2 5.5v13C2 20.4 3.6 22 5.5 22H16l6-6V5.5C22 3.6 20.4 2 18.5 2M7 12.5l1.3-1.4 2.1 2.1L15.6 8 17 9.4 10.5 16 7 12.5m8 7.5v-1.5c0-1.9 1.6-3.5 3.5-3.5H20l-5 5Z"></path></svg>');
   --md-admonition-icon--solution: url('data:image/svg+xml;charset=utf-8,<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M18.5 2h-13C3.6 2 2 3.6 2 5.5v13C2 20.4 3.6 22 5.5 22H16l6-6V5.5C22 3.6 20.4 2 18.5 2M7 12.5l1.3-1.4 2.1 2.1L15.6 8 17 9.4 10.5 16 7 12.5m8 7.5v-1.5c0-1.9 1.6-3.5 3.5-3.5H20l-5 5Z"></path></svg>');
@@ -240,3 +240,31 @@ h3 .enumerate-headings-plugin {
 .md-typeset table:not([class]) {
   font-size: 0.8rem;
 }
+
+/* YouTube video embeds */
+.md-typeset figure:has(.video-wrapper) {
+  width: 100%;
+}
+.video-wrapper {
+  position: relative;
+  display: block;
+  height: 0;
+  padding: 0;
+  overflow: hidden;
+  padding-bottom: 56.25%;
+}
+.video-wrapper > iframe {
+  position: absolute;
+  top: 0;
+  bottom: 0;
+  left: 0;
+  width: 100%;
+  height: 100%;
+  border: 0;
+}
+.youtube {
+  color: #ee0f0f;
+}
+.nextflow-primary {
+  color: #58bd9f;
+}
diff --git a/docs/hello_nextflow/00_orientation.md b/docs/hello_nextflow/00_orientation.md
@@ -1,5 +1,15 @@
 # Orientation
 
+<div class="video-wrapper">
+  <iframe width="560" height="315" src="https://www.youtube.com/embed/G3CV-FcV-rc?si=nyLvwhrSB2m1NPc5&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+</div>
+
+/// caption
+:fontawesome-brands-youtube:{ .youtube } See the [whole playlist on the Nextflow YouTube channel](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+///
+
+## GitHub Codespaces
+
 The GitHub Codespaces environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself.
 However, you do need a (free) GitHub account to log in, and you should take a few minutes to familiarize yourself with the interface.
 
diff --git a/docs/hello_nextflow/00_orientation.pt.md b/docs/hello_nextflow/00_orientation.pt.md
@@ -1,5 +1,13 @@
 # Orientação
 
+<div class="video-wrapper">
+  <iframe width="560" height="315" src="https://www.youtube.com/embed/G3CV-FcV-rc?si=nyLvwhrSB2m1NPc5&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+</div>
+
+/// caption
+:fontawesome-brands-youtube:{ .youtube } Veja a [playlist completa no canal de YouTube do Nextflow](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+///
+
 O ambiente GitHub Codespaces contém todo o software, código e dados necessários para este curso. Você não precisa instalar nada por conta própria. No entanto, é necessária uma conta (gratuita) para logar - e recomendamos que você reserve alguns minutos para se familiarizar com a interface.
 
 Caso ainda não tenha feito isso, siga [este link](../../envsetup/) antes de prosseguir.
diff --git a/docs/hello_nextflow/01_hello_world.md b/docs/hello_nextflow/01_hello_world.md
@@ -1,5 +1,13 @@
 # Part 1: Hello World
 
+<div class="video-wrapper">
+  <iframe width="560" height="315" src="https://www.youtube.com/embed/8X2hHI-9vms?si=F0t9LFYLjAWoyRXj&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+</div>
+
+/// caption
+:fontawesome-brands-youtube:{ .youtube } See the [whole playlist on the Nextflow YouTube channel](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+///
+
 In this first part of the Hello Nextflow training course, we ease into the topic with a very basic domain-agnostic Hello World example, which we'll progressively build up to demonstrate the usage of foundational Nextflow logic and components.
 
 !!! note
diff --git a/docs/hello_nextflow/01_hello_world.pt.md b/docs/hello_nextflow/01_hello_world.pt.md
@@ -1,5 +1,13 @@
 # Part 1: Hello World
 
+<div class="video-wrapper">
+  <iframe width="560" height="315" src="https://www.youtube.com/embed/8X2hHI-9vms?si=F0t9LFYLjAWoyRXj&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+</div>
+
+/// caption
+:fontawesome-brands-youtube:{ .youtube } Veja a [playlist completa no canal de YouTube do Nextflow](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+///
+
 Um exemplo "Hello World!" é um modelo minimalista projetado para demonstrar a sintaxe básica e a estrutura de uma linguagem de programação ou framework de software. Esse exemplo normalmente consiste em exibir a frase "Hello, World!" no dispositivo de saída, como o console ou terminal, ou gravá-la em um arquivo.
 
 Nesta primeira parte do curso de treinamento Hello Nextflow, introduzimos o tópico com um exemplo Hello World muito simples e independente de domínio, que será gradualmente expandido para demonstrar o uso dos componentes e da lógica fundamental do Nextflow.
diff --git a/docs/hello_nextflow/02_hello_channels.md b/docs/hello_nextflow/02_hello_channels.md
@@ -1,5 +1,13 @@
 # Part 2: Hello Channels
 
+<div class="video-wrapper">
+  <iframe width="560" height="315" src="https://www.youtube.com/embed/lJ41WMMm44M?si=xCItHLiOQWqoqBB9&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+</div>
+
+/// caption
+:fontawesome-brands-youtube:{ .youtube } See the [whole playlist on the Nextflow YouTube channel](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+///
+
 In Part 1 of this course (Hello World), we showed you how to provide a variable input to a process by providing the input in the process call directly: `sayHello(params.greet)`.
 That was a deliberately simplified approach.
 In practice, that approach has major limitations; namely that it only works for very simple cases where we only want to run the process once, on a single value.
diff --git a/docs/hello_nextflow/03_hello_workflow.md b/docs/hello_nextflow/03_hello_workflow.md
@@ -1,5 +1,13 @@
 # Part 3: Hello Workflow
 
+<div class="video-wrapper">
+  <iframe width="560" height="315" src="https://www.youtube.com/embed/zJP7cUYPEbA?si=Irl9nAQniDyICp2b&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+</div>
+
+/// caption
+:fontawesome-brands-youtube:{ .youtube } See the [whole playlist on the Nextflow YouTube channel](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+///
+
 Most real-world workflows involve more than one step.
 In this training module, you'll learn how to connect processes together in a multi-step workflow.
 
diff --git a/docs/hello_nextflow/04_hello_modules.md b/docs/hello_nextflow/04_hello_modules.md
@@ -1,5 +1,13 @@
 # Part 4: Hello Modules
 
+<div class="video-wrapper">
+  <iframe width="560" height="315" src="https://www.youtube.com/embed/Xxp_menS0E8?si=0AWnXB7xqHAzJdJV&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+</div>
+
+/// caption
+:fontawesome-brands-youtube:{ .youtube } See the [whole playlist on the Nextflow YouTube channel](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+///
+
 This section covers how to organize your workflow code to make development and maintenance of your pipeline more efficient and sustainable.
 Specifically, we are going to demonstrate how to use **modules**.
 
diff --git a/docs/hello_nextflow/05_hello_containers.md b/docs/hello_nextflow/05_hello_containers.md
@@ -1,5 +1,13 @@
 # Part 5: Hello Containers
 
+<div class="video-wrapper">
+  <iframe width="560" height="315" src="https://www.youtube.com/embed/5PyOWjKnNmg?si=QinuAnFwFj-Z8CrO&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+</div>
+
+/// caption
+:fontawesome-brands-youtube:{ .youtube } See the [whole playlist on the Nextflow YouTube channel](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+///
+
 In Parts 1-4 of this training course, you learned how to use the basic building blocks of Nextflow to assemble a simple workflow capable of processing some text, parallelizing execution if there were multiple inputs, and collecting the results for further processing.
 
 However, you were limited to basic UNIX tools available in your environment.
diff --git a/docs/hello_nextflow/06_hello_config.md b/docs/hello_nextflow/06_hello_config.md
@@ -1,5 +1,13 @@
 # Part 6: Hello Config
 
+<div class="video-wrapper">
+  <iframe width="560" height="315" src="https://www.youtube.com/embed/IuDO2HeKvXk?si=tnXTi6mRkITY0zW_&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+</div>
+
+/// caption
+:fontawesome-brands-youtube:{ .youtube } See the [whole playlist on the Nextflow YouTube channel](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+///
+
 This section will explore how to set up and manage the configuration of your Nextflow pipeline so that you'll be able to customize its behavior, adapt it to different environments, and optimize resource usage _without altering a single line of the workflow code itself_.
 
 There are multiple ways to do this; here we are going to use the simplest and most common configuration file mechanism, the `nextflow.config` file.
diff --git a/docs/hello_nextflow/index.md b/docs/hello_nextflow/index.md
@@ -16,6 +16,22 @@ Let's get started! Click on the "Open in GitHub Codespaces" button below to laun
 
 [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
 
+<h2>
+  <div style="float:right;">
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?si=9bz6-59u_0XFmHB0&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+  </div>
+
+Follow the videos
+
+</h2>
+
+The Hello Nextflow training has a video for each chapter, embedded at the top of each page.
+
+You can also find [the whole playlist on the Nextflow YouTube channel](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+
+<!-- Clearfix for float -->
+<div style="content: ''; clear: both; display: table;"></div>
+
 ## Learning objectives
 
 In this workshop, you will learn foundational concepts for building pipelines.
diff --git a/docs/hello_nextflow/index.pt.md b/docs/hello_nextflow/index.pt.md
@@ -16,6 +16,22 @@ Vamos começar!
 
 [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
 
+<h2>
+  <div style="float:right;">
+    <iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?si=9bz6-59u_0XFmHB0&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+  </div>
+
+Siga os vídeos
+
+</h2>
+
+A formação Hello Nextflow tem um vídeo para cada capítulo, incorporado no topo de cada página.
+
+Pode também encontrar [a playlist completa no canal de YouTube do Nextflow](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+
+<!-- Clearfix for float -->
+<div style="content: ''; clear: both; display: table;"></div>
+
 ## Objetivos de aprendizagem
 
 Neste workshop, você aprenderá conceitos fundamentais para a construção de pipelines.
diff --git a/docs/hello_nextflow/next_steps.md b/docs/hello_nextflow/next_steps.md
@@ -1,5 +1,13 @@
 # Next Steps
 
+<div class="video-wrapper">
+  <iframe width="560" height="315" src="https://www.youtube.com/embed/xHOcx_4Ancg?si=Lp8hS8RdaMwbp5j5&amp;list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+</div>
+
+/// caption
+:fontawesome-brands-youtube:{ .youtube } See the [whole playlist on the Nextflow YouTube channel](https://www.youtube.com/playlist?list=PLPZ8WHdZGxmXiHf8B26oB_fTfoKQdhlik).
+///
+
 Congrats again on completing the Hello Nextflow training course and thank you for completing our survey!
 
 **Here are our top 3 recommendations for what you can do next to take your Nextflow skills to the next level.**
diff --git a/docs/index.md b/docs/index.md
@@ -28,7 +28,7 @@ When you're ready to get down to work, click on the 'Open in GitHub Codespaces'
 
     !!! tip inline end ""
 
-        :material-lightbulb: Set up your environment for the first time.
+        :material-laptop:{.nextflow-primary} Set up your environment for the first time.
 
     Instructions for setting up your environment to work through training materials (all courses). Provides an orientation to GitHub Codespaces as well as alternate installation instructions for working on your own local machine.
 
@@ -42,7 +42,9 @@ These are foundational, domain-agnostic courses intended for those who are compl
 
     !!! tip inline end ""
 
-        :material-run-fast: Learn to develop pipelines in Nextflow.
+        :material-run-fast:{.nextflow-primary} Learn to develop pipelines in Nextflow.
+
+        :fontawesome-brands-youtube:{.youtube} Video material available.
 
     This is a course for newcomers who wish to learn how to develop their own pipelines. The course covers the core components of the Nextflow language in enough detail to enable developing simple but fully functional pipelines. It also covers key elements of pipeline design, development and configuration practices.
 
@@ -57,7 +59,7 @@ These are foundational, domain-agnostic courses intended for those who are compl
 
     !!! tip inline end ""
 
-        :material-run-fast: Learn to run Nextflow pipelines.
+        :material-run-fast:{.nextflow-primary} Learn to run Nextflow pipelines.
 
     This is a course for newcomers who wish to learn how to run existing pipelines. The course covers the bare essentials of the Nextflow language in order to enable interpretation of existing pipelines, as well as the mechanics for configuring and running Nextflow pipelines from a command-line environment. It also covers important components of the Nextflow ecosystem, including the nf-core project, which offers a large number of community-curated pipelines, and the Seqera platform for managing pipeline execution at scale (operated by the creators of Nextflow).
 
@@ -72,7 +74,7 @@ These are courses that demonstrate how to apply the concepts and components pres
 
     !!! tip inline end ""
 
-        :material-run-fast: Learn to develop a pipeline for genomics in Nextflow.
+        :material-dna:{.nextflow-primary} Learn to develop a pipeline for genomics in Nextflow.
 
     This is a course for researchers who wish to learn how to develop their own genomics pipelines. The course uses a variant calling use case to demonstrate how to develop a simple but functional genomics pipeline.
 
@@ -82,7 +84,7 @@ These are courses that demonstrate how to apply the concepts and components pres
 
     !!! tip inline end ""
 
-        :material-run-fast: Learn to develop a pipeline for RNAseq data processing in Nextflow.
+        :material-flask:{.nextflow-primary} Learn to develop a pipeline for RNAseq data processing in Nextflow.
 
     This is a course for researchers who wish to learn how to develop their own RNAseq pipelines. The course uses a bulk RNAseq processing use case to demonstrate how to develop a simple but functional RNAseq pipeline.
 
@@ -98,7 +100,7 @@ These are courses that demonstrate how to use Nextflow features in more detail o
 
     !!! tip inline end ""
 
-        :material-run-fast: Training modules for a variety of topics of interest.
+        :material-compass:{.nextflow-primary} Training modules for a variety of topics of interest.
 
     This is a course for Nextflow developers who wish to widen their range and/or deepen their skills. Although the modules are presented linearly, learners are welcome to pick and choose topics in any order. Any dependencies on components/skills that go beyond the scope of the 'Hello Nextflow' course are indicated in the corresponding module overview.
 
@@ -108,7 +110,7 @@ These are courses that demonstrate how to use Nextflow features in more detail o
 
     !!! quote inline end ""
 
-        :material-lightbulb: Comprehensive training material for exploring the full scope of Nextflow's capabilities.
+        :octicons-mortar-board-16:{.nextflow-primary} Comprehensive training material for exploring the full scope of Nextflow's capabilities.
 
     The fundamentals training material covers all things Nextflow. Intended as a reference material for anyone looking to build complex workflows with Nextflow.
 
@@ -118,7 +120,7 @@ These are courses that demonstrate how to use Nextflow features in more detail o
 
     !!! quote inline end ""
 
-        :material-lightbulb: Advanced training material for mastering Nextflow.
+        :fontawesome-solid-hat-wizard:{.nextflow-primary} Advanced training material for mastering Nextflow.
 
     Advanced material exploring the more advanced features of the Nextflow language and runtime, and how to use them to write efficient and scalable data-intensive workflows.
 
diff --git a/mkdocs.yml b/mkdocs.yml
diff --git a/requirements.txt b/requirements.txt
