Port Adam's nf-test to new structure

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

@@ -1,51 +1,55 @@
 # Gitpod
 
-Gitpod is a cloud development environment for teams to efficiently and securely develop software. It can improve your developer experience by coding in a cloud development environment.
+Gitpod is a cloud-based development environment for teams to efficiently and securely develop software.
+We use it to provide a consistent training environment for everyone.
 
 ## Creating a Gitpod account
 
-You can create a free [Gitpod](https://gitpod.io/) account using your GitLab, GitHub, or Bitbucket account.
+You can create a free [Gitpod](https://gitpod.io/) account from the [Gitpod login page](https://gitpod.io/login/).
 
-You can create an account using the [Gitpod login page](https://gitpod.io/login/).
+You will be prompted to choose between 'Gitpod Flex' and 'Gitpod Classic'.
+Select 'Gitpod Classic' and click 'Continue'.
 
-![Gitpod log in](img/login.png)
-
-It is best to connect your LinkedIn account to receive a full 50 hours usage allocation.
+![Select 'Gitpod Classic'](img/select_gitpod_classic.png)
 
-![Gitpod log in one step](img/onestepaway.png)
+Next, log in using your GitHub account.
 
-After selecting your preferred editor, theme, and profile details, click continue and your account will be created and ready to use.
+![Gitpod log in](img/login.png)
 
-!!! note
+You may need to fill out an additional form or two.
+When prompted to connect a LinkedIn account, we recommend doing so if you have one, to receive the extra 50 hours usage allocation.
+Don't worry too much if you don't have one; the basic allocation is more than enough to work through the introductory training course.
 
-    It is recommended to use the VS code editor.
+If you are prompted to select your preferred editor, we strongly recommend choosing the VSCode editor, as that is what we use for Nextflow development in general and for trainings in particular.
 
 ## Running Gitpod
 
-Click the following URL to run Gitpod: <https://gitpod.io/#https://github.com/nextflow-io/training>
+Once you are logged in to Gitpod, open this link in your browser to open the training environment: <https://gitpod.io/#https://github.com/nextflow-io/training>
 
-This URL is the Nextflow training repository prefixed with `https://gitpod.io/#`.
+This URL is the address to the Nextflow training repository prefixed with `https://gitpod.io/#`.
 
-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 Gitpod](https://img.shields.io/badge/Gitpod-%20Open%20in%20Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/nextflow-io/training)
 
 If you are already logged in, your Gitpod environment will start to load.
 
 ### Explore your Gitpod IDE
 
-After Gitpod has loaded, you should see something similar to the following:
+After Gitpod has loaded, you should see something similar to the following (which may in light mode depending on your account preferences):
 
 ![Gitpod welcome](img/gitpod.welcome.png)
 
+This is the interface of the VSCode IDE, a popular code development application that we recommend using for Nextflow development.
+
 - **The sidebar** allows you to customize your Gitpod environment and perform basic tasks (copy, paste, open files, search, git, etc.). You can click the explorer button to see which files are in this repository.
 - **The terminal** allows you to run all the programs in the repository. For example, both `nextflow` and `docker` are installed and can be executed.
 - **The file explorer** allows you to view and edit files. Clicking on a file in the explorer will open it within the main window.
-- **The Simple Browser** lets you view the nf-training material browser (<https://training.nextflow.io/>). If you close it by accident, you can load the simple browser again by typing the following in the terminal: `gp preview https://training.nextflow.io`.
+- **The Simple Browser** lets you view the training instructions in a web browser (<https://training.nextflow.io/>). If you close it by accident, you can load the simple browser again by typing the following in the terminal: `gp preview https://training.nextflow.io`.
 
 ### Gitpod resources
 
-Gitpod gives you 500 free credits per month, which is equivalent to 50 hours of free environment runtime using the standard workspace (up to 4 cores, 8 GB RAM, and 30 GB storage).
+Gitpod gives you up to 500 free credits per month, which is equivalent to 50 hours of free environment runtime using the standard workspace (up to 4 cores, 8 GB RAM, and 30 GB storage).
 
 There is also a large workspace option that gives you up to 8 cores, 16GB RAM, and 50GB storage. However, the large workspace will use your free credits quicker and you will have fewer hours of access to this space.
 

docs/envsetup/02_local.md

@@ -1,6 +1,6 @@
 # Local installation
 
-If you **can not** access Gitpod you can also install everything locally.
+If you **cannot** use Gitpod for any reason, you have the option of installing everything locally instead.
 
 Some requirements may be different depending on your local machine.
 
@@ -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/hello_nextflow/01_orientation.md → docs/hello_nextflow/00_orientation.md

@@ -1,16 +1,16 @@
 # Orientation
 
-The Gitpod environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself.
+The training 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) account to log in, and you should take a few minutes to familiarize yourself with the interface.
 
 If you have not yet done so, please follow [this link](../../envsetup/) before going any further.
 
 ## Materials provided
 
-Throughout this training course, we'll be working in the `hello-nextflow/` directory, which loads by default when you open the Gitpod 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 Gitpod 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
-│   └── 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
 ```
 
-!!!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 /workspace/gitpod/hello-nextflow