New multi-course structure for training materials (#486)

Major refresh of the training materials

* Pared down and streamlined the Hello Nextflow course (v2)
* Spun out the genomics material into a separate mini-course, Nextflow for Genomics
* Added stubs/placeholders for Nextflow Run and Side Quests
* Consolidated the experimental and/or unfinished content into `other/`
* Updated and streamlined the training index

---------

Co-authored-by: Jonathan Manning <[email protected]>
Co-authored-by: Rob Syme <[email protected]>
Co-authored-by: Marcel Ribeiro-Dantas <[email protected]>
Co-authored-by: Marcel Ribeiro-Dantas <[email protected]>
Co-authored-by: Phil Ewels <[email protected]>

Author: 5 people

CONTRIBUTING.md

@@ -138,7 +138,7 @@ Please see the [official docs](https://squidfunk.github.io/mkdocs-material/refer
 
 - Note that we have two custom admonitions: `exercise` and `result` (alias `solution`).
 - `!!!` does a regular admonition, `???` makes it collapsed (click to expand).
-- Intendation is important! Make sure you check the rendered site, as it's easy to make a mistake.
+- Indentation is important! Make sure you check the rendered site, as it's easy to make a mistake.
 
 ## Known limitations
 

docs/advanced/index.md

@@ -2,9 +2,10 @@
 
 Welcome to our Nextflow workshop for intermediate and advanced users!
 
-In this workshop, we will explore the advanced features of the Nextflow language and runtime, and learn how to use them to write efficient and scalable data-intensive workflows. We will cover topics such as parallel execution, error handling, and workflow customization.
+In this workshop, we will explore the advanced features of the Nextflow language and runtime, and learn how to use them to write efficient and scalable data-intensive workflows.
+We will cover topics such as parallel execution, error handling, and workflow customization.
 
-Please note that this is not an introductory workshop, and we will assume some basic familiarity with Nextflow.
+Please note that this is not an introductory workshop, and we will assume extensive familiarity with Nextflow.
 
 By the end of this workshop, you will have the skills and knowledge to create complex and powerful Nextflow pipelines for your own data analysis projects.
 
@@ -34,9 +35,12 @@ Please note that this is **not** a beginner's workshop and familiarity with Next
 - Familiarity with Nextflow and Groovy
 - An understanding of common file formats
 
-## Follow the training video
+## Follow the training videos and get help
 
-We run a free online training event for this course approximately every six months. Videos are streamed to YouTube and questions are handled in the nf-core Slack community. You can watch the recording of the most recent training ([September, 2023](https://nf-co.re/events/2023/training-sept-2023/)) below:
+Video recordings are available for this course.
+You can ask questions in the [Seqera community forum](https://community.seqera.io/).
+
+You can watch the recording of the most recent training ([September, 2023](https://nf-co.re/events/2023/training-sept-2023/)) below:
 
 <div style="text-align: center;">
     <iframe width="560" height="315" src="https://www.youtube.com/embed/nPAH9owvKvI?si=Kt3WmxF7rGhRp2L1" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen="" data-ruffle-polyfilled=""></iframe>

docs/basic_training/cache_and_resume.md

@@ -349,7 +349,7 @@ So D is matched with 'a' here, which was not the intention. That order will like
 
     ??? solution
 
-        You should see that while FOO and BAR reliably re-use their cache, FOOBAR will re-run at least a subset of its tasks due to differences in the combinations of inputs it recieves.
+        You should see that while FOO and BAR reliably re-use their cache, FOOBAR will re-run at least a subset of its tasks due to differences in the combinations of inputs it receives.
 
         The output will look like this:
 

docs/basic_training/index.md

@@ -1,6 +1,7 @@
 # Fundamentals Training
 
-You are now on the path to writing reproducible and scalable scientific workflows using Nextflow. This guide complements the full [Nextflow documentation](https://www.nextflow.io/docs/latest) - if you ever have any doubts, please refer to that.
+You are now on the path to writing reproducible and scalable scientific workflows using Nextflow.
+This guide complements the full [Nextflow documentation](https://www.nextflow.io/docs/latest) - if you ever have any doubts, please refer to that.
 
 Let's get started!
 
@@ -18,17 +19,21 @@ By the end of this course you should:
 
 ## Audience & prerequisites
 
-Please note that this is **not** a beginner's workshop and familiarity with Nextflow, the command line, and common file formats is assumed.
+Please note that this is **not** a beginner's workshop.
+Familiarity with Nextflow, the command line, and common file formats is assumed.
+
+For a beginner's introduction to Nextflow, please see the [Hello Nextflow](../hello_nextflow/) course.
 
 **Prerequisites**
 
 - A GitHub account
 - Experience with command line
 - An understanding of common file formats
 
-## Follow the training videos
+## Follow the training videos and get help
 
-Free online training events for this course are run approximately every six months. Videos are streamed to YouTube and questions are handled in the nf-core Slack community.
+Video recordings are available for this course.
+You can ask questions in the [Seqera community forum](https://community.seqera.io/).
 
 You can watch the recording of the most recent training ([March, 2024](https://nf-co.re/events/2024/training-foundational-march)) in the [YouTube playlist](https://youtu.be/dbOKB3VRpuE?si=MYBy4-gjRfEYkVRM) below:
 
@@ -38,7 +43,7 @@ You can watch the recording of the most recent training ([March, 2024](https://n
 
 !!! warning
 
-    Please note that the training material is updated regularly and that the videos may be out of date.
+    Please note that the training material is updated regularly and that the videos linked below may be out of date.
 
 If English is not your preferred language, you may find it useful to follow the training from the [March 2023 event](https://nf-co.re/events/2023/training-march-2023), which is available in multiple languages.
 

docs/envsetup/01_setup.md

@@ -11,7 +11,7 @@ You can create a free GitHub account from the [GitHub home page](https://github.
 
 Once you are logged in to GitHub, open this link in your browser to open the training environment: <https://codespaces.new/nextflow-io/training?quickstart=1&ref=master>
 
-Alternatively, you can click on the button below.
+Alternatively, you can click on the button shown below from the many pages in the training portal where it is displayed.
 
 [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
 
@@ -34,7 +34,7 @@ The free Github plan includes 120 core-hours of Codespaces compute per month, wh
 
 ## Explore your GitHub Codespaces IDE
 
-After GitHub Codespaces has loaded, you should see something similar to the following (which may in light mode depending on your account preferences):
+After GitHub Codespaces has loaded, you should see something similar to the following (which may open in light mode depending on your account preferences):
 
 ![GitHub Codespaces welcome](img/codespaces_welcome.png)
 
@@ -65,6 +65,10 @@ You should see the previous session, the default option is to resume it:
 
 ![Resume a GitHub Codespace](img/codespaces_resume.png)
 
+## Saving files from GitHub Codespaces to your local machine
+
+To save any file from the explorer panel, right-click the file and select `Download`.
+
 ## GitHub Codespaces quotas
 
 GitHub Codespaces gives you up to 15 GB-month storage per month, and 120 core-hours per month.
@@ -76,7 +80,3 @@ Optionally, you can purchase access to more resources.
 
 More information can be found in the GitHub docs:
 [About billing for GitHub Codespaces](https://docs.github.com/en/billing/managing-billing-for-your-products/managing-billing-for-github-codespaces/about-billing-for-github-codespaces)
-
-## Saving files from GitHub Codespaces to your local machine
-
-To save any file from the explorer panel, right-click the file and select `Download`.

docs/envsetup/02_local.md

@@ -59,7 +59,7 @@ To download the material, execute this command:
 git clone https://github.com/nextflow-io/training.git
 ```
 
-Then `cd` into the `nf-training` directory.
+Then `cd` into the relevant directory. By default, that is `hello-nextflow`.
 
 ## Checking your installation
 
@@ -79,7 +79,7 @@ This should print the current version, system, and runtime.
     nextflow info
     ```
 
-    This should come up with the Nextflow version and runtime information:
+    This should come up with the Nextflow version and runtime information (actual versions may differ):
 
     ```console
     Version: 23.10.1 build 5891

docs/envsetup/img/onestepaway.png

@@ -7,10 +7,10 @@ If you have not yet done so, please follow [this link](../../envsetup/) before g
 
 ## Materials provided
 
-Throughout this training course, we'll be working in the `hello-nextflow/` directory, which loads by default when you open the GitHub Codespaces workspace.
+Throughout this training course, we'll be working in the `hello-nextflow/` directory, which loads by default when you open the training workspace.
 This directory contains all the code files, test data and accessory files you will need.
 
-Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left-hand side of the GitHub Codespaces workspace.
+Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left-hand side of the training workspace.
 Alternatively, you can use the `tree` command.
 Throughout the course, we use the output of `tree` to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity.
 
@@ -24,64 +24,36 @@ If you run this inside `hello-nextflow`, you should see the following output:
 
 ```console title="Directory contents"
 .
-├── containers
-│   ├── build
-│   ├── data
-│   ├── results
-│   └── solutions
-├── data
-│   ├── bam
-│   ├── greetings.csv
-│   ├── ref
-│   ├── sample_bams.txt
-│   └── samplesheet.csv
-├── hello-config
-│   ├── demo-params.json
-│   ├── main.nf
-│   └── nextflow.config
+├── greetings.csv
+├── hello-channels.nf
+├── hello-config.nf
 ├── hello-containers.nf
-├── hello-genomics.nf
-├── hello-modules
-│   ├── demo-params.json
-│   ├── main.nf
-│   └── nextflow.config
-├── hello-nf-core
-│   ├── data
-│   └── solution
-├── hello-nf-test
-│   ├── demo-params.json
-│   ├── main.nf
-│   ├── modules
-│   └── nextflow.config
-├── hello-operators.nf
+├── hello-modules.nf
+├── hello-workflow.nf
 ├── hello-world.nf
 ├── nextflow.config
-└── solutions
-    ├── hello-config
-    ├── hello-genomics
-    ├── hello-modules
-    ├── hello-nf-test
-    ├── hello-operators
-    └── hello-world
-
-22 directories, 17 files
+├── solutions
+│   ├── 1-hello-world
+│   ├── 2-hello-channels
+│   ├── 3-hello-workflow
+│   ├── 4-hello-modules
+│   ├── 5-hello-containers
+│   └── 6-hello-config
+└── test-params.json
+
+7 directories, 9 files
 ```
 
-!!!note
-
-    Don't worry if this seems like a lot; we'll go through the relevant pieces at each step of the course.
-    This is just meant to give you an overview.
-
 **Here's a summary of what you should know to get started:**
 
 - **The `.nf` files** are workflow scripts that are named based on what part of the course they're used in.
 
-- **The `hello-*` directories** are directories used in the later Parts of the course where we are working with more than just one workflow file.
-
 - **The file `nextflow.config`** is a configuration file that sets minimal environment properties.
   You can ignore it for now.
 
-- **The `data` directory** contains the input data we'll use in most of the course. The dataset is described in detail in Part 3, when we introduce it for the first time.
+- **The file `greetings.csv`** contains input data we'll use in most of the course. It is described in Part 1, when we introduce it for the first time.
+
+- **The file `test-params.json`** is a file we'll use in Part 6. You can ignore it for now.
 
 - **The `solutions` directory** contains the completed workflow scripts that result from each step of the course.
   They are intended to be used as a reference to check your work and troubleshoot any issues.
@@ -90,7 +62,7 @@ If you run this inside `hello-nextflow`, you should see the following output:
 
 !!!tip
 
-    If for whatever reason you move out of this directory, you can always run this command to return to it:
+    If for whatever reason you move out of this directory, you can always run this command to return to it (within the training environment):
 
     ```bash
     cd /workspaces/training/hello-nextflow

docs/hello_nextflow/01_orientation.md renamed to docs/hello_nextflow/00_orientation.md

@@ -1,6 +1,6 @@
 # Orientação
 
-O ambiente Gitpod 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.
+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.
 
@@ -20,47 +20,24 @@ Se você executar isso dentro do diretório `hello-nextflow`, verá a seguinte s
 
 ```console title="Directory contents"
 .
-├── containers
-│   ├── build
-│   ├── data
-│   ├── results
-│   └── scripts
-├── data
-│   ├── bam
-│   ├── greetings.csv
-│   ├── ref
-│   ├── sample_bams.txt
-│   └── samplesheet.csv
-├── hello-config
-│   ├── demo-params.json
-│   ├── main.nf
-│   └── nextflow.config
+├── greetings.csv
+├── hello-channels.nf
+├── hello-config.nf
 ├── hello-containers.nf
-├── hello-genomics.nf
-├── hello-modules
-│   ├── demo-params.json
-│   ├── main.nf
-│   └── nextflow.config
-├── hello-nf-core
-│   ├── data
-│   └── solution
-├── hello-nf-test
-│   ├── demo-params.json
-│   ├── main.nf
-│   ├── modules
-│   └── nextflow.config
-├── hello-operators.nf
+├── hello-modules.nf
+├── hello-workflow.nf
 ├── hello-world.nf
 ├── nextflow.config
-└── solutions
-    ├── hello-config
-    ├── hello-genomics
-    ├── hello-modules
-    ├── hello-nf-test
-    ├── hello-operators
-    └── hello-world
-
-18 directories, 17 files
+├── solutions
+│   ├── 1-hello-world
+│   ├── 2-hello-channels
+│   ├── 3-hello-workflow
+│   ├── 4-hello-modules
+│   ├── 5-hello-containers
+│   └── 6-hello-config
+└── test-params.json
+
+7 directories, 9 files
 ```
 
 !!!nota
@@ -71,11 +48,11 @@ Se você executar isso dentro do diretório `hello-nextflow`, verá a seguinte s
 
 - **Os arquivos `.nf`** são _scripts_ de fluxo de trabalho nomeados com base na parte do curso em que são utilizados.
 
-- **Os diretórios `hello-*`** são usados nas partes posteriores do curso, onde trabalhamos com mais de um arquivo de fluxo de trabalho.
-
 - **O arquivo `nextflow.config`** é um arquivo de configuração que define propriedades mínimas do ambiente. Você pode ignorá-lo por enquanto.
 
-- **O diretório `data`** contém os dados de entrada que usaremos na maior parte do curso. O conjunto de dados é descrito em detalhe na Parte 3, quando o introduzimos pela primeira vez.
+- **The file `greetings.csv`** contains input data we'll use in most of the course. It is described in Part 1, when we introduce it for the first time.
+
+- **The file `test-params.json`** is a file we'll use in Part 6. You can ignore it for now.
 
 - **O diretório `solutions`** contém os _scripts_ de fluxo de trabalho completos resultantes de cada etapa do curso. Eles servem como referência para verificar seu trabalho e solucionar quaisquer problemas. As informações de nome e o número presentes no nome do arquivo correspondem à etapa da parte relevante do curso. Por exemplo, o arquivo `hello-world-4.nf` é o resultado esperado ao completar as etapas 1 a 4 da Parte 1: Hello World.