Merge branch 'dev' into feat/hello-seqera

Author: kenibrewer

.devcontainer/devcontainer.json

@@ -1,10 +1,14 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
+    "image": "ghcr.io/nextflow-io/training:latest",
     "remoteUser": "gitpod",
-
-    "postCreateCommand": "pre-commit install --install-hooks",
-
+    "features": {
+        "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
+    },
+    "remoteEnv": {
+        "NXF_HOME": "/workspaces/.nextflow",
+        "HOST_PROJECT_PATH": "${localWorkspaceFolder}"
+    },
     // Configure tool-specific properties.
     "customizations": {
         // Configure properties specific to VS Code.
@@ -13,7 +17,6 @@
             "settings": {
                 "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
-
             // Add the IDs of extensions you want installed when the container is created.
             "extensions": [
                 "ms-python.python",

docs/assets/overrides/partials/toc.html

@@ -371,7 +371,7 @@ else {
 The `else` branch is optional. Also, the curly brackets are optional when the branch defines just a single statement.
 
 ```groovy linenums="1" title="snippet.nf"
-x = 1
+x = 11
 if (x > 10)
     println 'Hello'
 ```

docs/basic_training/groovy.md

@@ -254,11 +254,15 @@ else {
 O ramo `else` é opcional. Além disso, as chaves são opcionais quando a ramificação define apenas uma única instrução.
 
 ```groovy linenums="1"
-x = 1
+x = 11
 if (x > 10)
     println 'Olá'
 ```
 
+```console title="Output"
+Olá
+```
+
 !!! tip
 
     `null`, strings vazias e coleções (mapas e listas) vazias são avaliadas como `false`.

docs/basic_training/groovy.pt.md

@@ -1,80 +1,93 @@
 # Orientation
 
-The Gitpod environment contains some test data that will be used in this training course. All software required is already installed and configured in it too.
+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.
+However, you do need a (free) account to log in, and you should take a few minutes to familiarize yourself with the interface.
 
-!!! note
-
-    Follow [this link](../../envsetup/) if you have not yet set up your Gitpod environment.
+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.
+Throughout this training course, we'll be working in the `hello-nextflow/` directory, which loads by default when you open the Gitpod workspace.
+This directory contains all the code files, test data and accessory files you will need.
 
-```bash
-cd /workspace/gitpod/hello-nextflow
-```
+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.
+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.
 
-This directory contains all the code files, test data and accessory files you will need. Feel free to explore the contents of this directory; an easy way to see what it contains is the use the `tree` command (here we generate a table of contents to the second level down).
+Here we generate a table of contents to the second level down:
 
 ```bash
 tree . -L 2
 ```
 
-You should see the following output:
+If you run this inside `hello-nextflow`, you should see the following output:
 
 ```console title="Directory contents"
-/workspace/gitpod/hello-nextflow
+.
+├── containers
+│   ├── build
+│   ├── data
+│   ├── results
+│   └── scripts
 ├── data
 │   ├── bam
 │   ├── greetings.csv
 │   ├── ref
 │   ├── sample_bams.txt
 │   └── samplesheet.csv
-├── hello-gatk.nf
-├── hello-modules.nf
-├── hello-nf-test.nf
+├── hello-config
+│   ├── demo-params.json
+│   ├── main.nf
+│   └── nextflow.config
+├── hello-containers.nf
+├── hello-genomics.nf
+├── hello-modules
+│   ├── demo-params.json
+│   ├── main.nf
+│   └── nextflow.config
+├── hello-nf-test
+│   ├── demo-params.json
+│   ├── main.nf
+│   └── nextflow.config
+├── hello-operators.nf
 ├── hello-world.nf
 ├── nextflow.config
-└── scripts
-    ├── hello-config-1.config
-    ├── hello-config-2.config
-    ├── hello-config-3.config
-    ├── hello-config-4.config
-    ├── hello-gatk-1.nf
-    ├── hello-gatk-2.nf
-    ├── hello-gatk-3.nf
-    ├── hello-gatk-4.nf
-    ├── hello-gatk-5.nf
-    ├── hello-gatk-6.nf
-    ├── hello-modules-1.nf
-    ├── hello-modules-2.nf
-    ├── hello-modules-3.nf
-    ├── hello-world-1.nf
-    ├── hello-world-2.nf
-    ├── hello-world-3.nf
-    ├── hello-world-4.nf
-    ├── hello-world-5.nf
-    ├── hello-world-6.nf
-    ├── hello-world-7.nf
-    ├── hello-world-8.nf
-    ├── hello-world-9.nf
-    ├── modules
-    └── nextflow.config
-
-13 directories, 48 files
-
+└── solutions
+    ├── hello-config
+    ├── hello-genomics
+    ├── hello-modules
+    ├── hello-nf-test
+    ├── hello-operators
+    └── hello-world
+
+18 directories, 17 files
 ```
 
-**The `data` directory** contains the input data we'll use in Part 3: Hello Genomics, which uses an example from genomics to demonstrate how to build a simple analysis pipeline.
-The data are described in detail in that section of the course.
+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 `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.
+The name and number in the filename correspond to the step of the relevant part of the course.
+For example, the file `hello-world-4.nf` is the expected result of completing steps 1 through 4 of Part 1: Hello World.
 
-**The file `hello-world.nf`** is a simple but fully functional workflow script that serves as a starting point to Part 1: Hello World.
+!!!tip
 
-**The file `hello-gatk.nf`** is a stub that serves as a starting point to Part 3: Hello Genomics.
-In its initial state, it is NOT a functional workflow script.
+    If for whatever reason you move out of this directory, you can always run this command to return to it:
 
-**The remaining `.nf` files** are functional workflow scripts that serve as starting points for the corresponding parts of the course.
+    ```bash
+    cd /workspace/gitpod/hello-nextflow
+    ```
 
-**The `scripts` 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. The name and number in the filename correspond to the step of the relevant part of the course. For example, the file `hello-world-4.nf` is the expected result of completing steps 1 through 4 of Part 1: Hello World.
+Now, to begin the course, click on the arrow in the bottom right corner of this page.

docs/hello_nextflow/01_orientation.md

@@ -411,7 +411,6 @@ Let's write a new process to define how that's going to work, based on the comma
 process GATK_GENOMICSDB {
 
     container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867"
-
     publishDir 'results_genomics', mode: 'copy'
 
     input:
@@ -736,8 +735,8 @@ _Before:_
 
 ```groovy title="hello-operators.nf" linenums="78"
 input:
-    path all_gvcfs_ch
-    path all_idxs_ch
+    path all_gvcfs
+    path all_idxs
     path interval_list
     val cohort_name
 ```
@@ -746,8 +745,8 @@ _After:_
 
 ```groovy title="hello-operators.nf" linenums="78"
 input:
-    path all_gvcfs_ch
-    path all_idxs_ch
+    path all_gvcfs
+    path all_idxs
     path interval_list
     val cohort_name
     path ref_fasta