Migrate hello_nf-core to nf-core tools 4.0.2 + v2 parser

.devcontainer/local-features/uv-tools/install.sh

@@ -3,5 +3,5 @@
 # Install python cli tools using uv
 
 uv tool install pre-commit
-uv tool install nf-core==3.5.2
+uv tool install nf-core==4.0.2
 uv tool install "mkdocs-quiz>=1.5.2"

docs/en/docs/hello_nf-core/00_orientation.md

@@ -20,28 +20,20 @@ If you are working through this course by yourself, please acquaint yourself wit
 
 ### Version requirements
 
-This training works with **Nextflow 25.10.2** or later and **requires the v1 syntax parser**, because the nf-core conventions used in this course are not yet compatible with the v2 parser.
-From Nextflow 26.04 the v2 parser is the default, so you must explicitly select v1 as shown below.
+This training works with Nextflow 25.10.2 or later **with the v2 syntax parser**, which is the default from Nextflow 26.04 onward.
+In our training environment you don't need to do anything: it runs Nextflow 26.04.4 with the v2 parser. If you are using a local or custom environment, see the [version notes](../info/nxf_versions.md).
 
-#### If you are using our training environment:
-
-You MUST run the following command before going any further:
-
-```bash
-export NXF_SYNTAX_PARSER=v1
-```
-
-On Nextflow 26.04 and later this is essential: it overrides the v2 parser that those versions enable by default (our training environment sets `NXF_SYNTAX_PARSER=v2` for the other courses).
-
-#### If you are using a local or custom environment:
-
-Please make sure you are using the correct settings as documented [here](../info/nxf_versions.md).
-
-The training additionally requires **nf-core tools 3.5.2**.
+This training additionally requires **nf-core tools 4.0.2**.
 If you use a different version of nf-core tooling, you may have difficulty following along.
 
 You can check what version is installed in your environment using the command `nf-core --version`.
 
+!!! warning "v2 parser compatibility"
+
+    Many nf-core pipelines do not yet support the v2 syntax parser.
+    If you run an nf-core pipeline other than those used in this course and encounter errors, you may need to switch to the v1 parser by setting `export NXF_SYNTAX_PARSER=v1`.
+    See the [version notes](../info/nxf_versions.md) for details.
+
 ## Get ready to work
 
 Once your codespace is running, there are two things you need to do before diving into the training: set your working directory for this specific course, and take a look at the materials provided.
@@ -83,7 +75,10 @@ tree . -L 2
 
     ```console
     .
+    ├── custom.config
     ├── greetings.csv
+    ├── malformed_samplesheet.csv
+    ├── my_params.yml
     ├── original-hello
     │   ├── hello.nf
     │   ├── modules
@@ -102,6 +97,12 @@ We use collapsible sections like this to include expected command output in a co
 
 - **The `greetings.csv` file** is a CSV containing some minimal columnar data we use for testing purposes.
 
+- **The `custom.config` file** is an example Nextflow configuration file used in Part 1 to demonstrate process resource overrides and `ext.args`.
+
+- **The `malformed_samplesheet.csv` file** is an intentionally broken samplesheet used in Part 1 to demonstrate input validation.
+
+- **The `my_params.yml` file** is an example params file used in Part 1 to demonstrate how to pass boolean parameters to a pipeline.
+
 - **The `original-hello` directory** contains a copy of the source code produced by working through the complete Hello Nextflow training series (with Docker enabled).
 
 - **The `solutions` directory** contains the completed workflow scripts that result from each step of the course.
@@ -113,7 +114,7 @@ Think you're ready to dive in?
 
 - [ ] I understand the goal of this course and its prerequisites
 - [ ] My environment is up and running
-- [ ] I've made certain that the syntax parser is set to **v1**
+- [ ] I'm using nf-core tools 4.0.2 (check with `nf-core --version`)
 - [ ] I've set my working directory appropriately
 
 If you can check all the boxes, you're good to go.