Enable local use via multi devcontainer

.devcontainer/codespaces/devcontainer.json

@@ -0,0 +1,42 @@
+{
+    "name": "codespaces",
+    "build": {
+        "dockerfile": "Dockerfile",
+        "context": ".."
+    },
+    "remoteUser": "gitpod",
+    "features": {
+        "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
+    },
+    "workspaceFolder": "/workspaces/training",
+    "workspaceMount": "source=${localWorkspaceFolder},target=/workspaces/training,type=bind", // Used for local devcontainers, ignored in Codespaces.
+    "remoteEnv": {
+        "NXF_HOME": "/workspaces/.nextflow",
+        "HOST_PROJECT_PATH": "/workspaces/training" //Codespaces and local devcontainers will both work with this.
+    },
+    "postCreateCommand": "if [ -z \"$CODESPACES\" ]; then echo \"Local Development\"; else echo \"Codespaces Development\"; fi",
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
+            },
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": [
+                "ms-python.python",
+                "ms-python.vscode-pylance",
+                "nf-core.nf-core-extensionpack",
+                "nextflow.nextflow",
+                "codezombiech.gitignore"
+            ]
+        }
+    },
+    "portsAttributes": {
+        "3000": {
+            "label": "Application",
+            "onAutoForward": "openPreview"
+        }
+    }
+}

.devcontainer/devcontainer.json

@@ -0,0 +1 @@
+./codespaces/devcontainer.json

.devcontainer/local/devcontainer.json

@@ -0,0 +1,45 @@
+{
+    "name": "local",
+    "build": {
+        "dockerfile": "Dockerfile",
+        "context": ".."
+    },
+    "remoteUser": "gitpod",
+    "features": {
+        "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
+    },
+    "workspaceFolder": "${localWorkspaceFolder}",
+    "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind",
+    "remoteEnv": {
+        "NXF_HOME": "/workspaces/training/.nextflow",
+        "HOST_PROJECT_PATH": "/workspaces/training"
+    },
+    "postCreateCommand": "sudo mkdir -p /workspaces && sudo ln -s ${localWorkspaceFolder} /workspaces/training && if [ -z \"$CODESPACES\" ]; then echo \"Local Development\"; else echo \"Codespaces Development\"; fi",
+    "postAttachCommand": "cd /workspaces/training",
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python",
+                "terminal.integrated.cwd": "/workspaces/training",
+                "terminal.integrated.defaultLocation": "workspace"
+            },
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": [
+                "ms-python.python",
+                "ms-python.vscode-pylance",
+                "nf-core.nf-core-extensionpack",
+                "nextflow.nextflow",
+                "codezombiech.gitignore"
+            ]
+        }
+    },
+    "portsAttributes": {
+        "3000": {
+            "label": "Application",
+            "onAutoForward": "openPreview"
+        }
+    }
+}

docs/hello_nextflow/01_hello_world.md

@@ -138,7 +138,7 @@ process sayHello {
 }
 ```
 
-This a very minimal process definition that just contains an `output` definition and the `script` to execute.
+This is a very minimal process definition that just contains an `output` definition and the `script` to execute.
 
 The `output` definition includes the `path` qualifier, which tells Nextflow this should be handled as a path (includes both directory paths and files).
 Another common qualifier is `val`.
@@ -172,7 +172,7 @@ workflow {
 }
 ```
 
-This a very minimal **workflow** definition.
+This is a very minimal **workflow** definition.
 In a real-world pipeline, the workflow typically contains multiple calls to **processes** connected by **channels**, and the processes expect one or more variable **input(s)**.
 
 You'll learn how to add variable inputs later in this training module; and you'll learn how to add more processes and connect them by channels in Part 3 of this course.
@@ -479,7 +479,7 @@ In the process block, make the following code change:
 
 _Before:_
 
-```groovy title="hello-channels.nf" linenums="6"
+```groovy title="hello-world.nf" linenums="6"
 process sayHello {
 
     publishDir 'results', mode: 'copy'
@@ -490,7 +490,7 @@ process sayHello {
 
 _After:_
 
-```groovy title="hello-channels.nf" linenums="6"
+```groovy title="hello-world.nf" linenums="6"
 process sayHello {
 
     publishDir 'results', mode: 'copy'

docs/hello_nextflow/02_hello_channels.md

@@ -522,7 +522,7 @@ Here we added the operator on the next line for readability, but you can add ope
 
 #### 3.2.2. Add `view()` to inspect channel contents
 
-We could run this right away to test if it works, but while we're at it, we're also going to add a couple of [`view()`](https://www.nextflow.io/docs/latest/reference/operator.html#view) directives, which allow us to inspect the contents of a channel.
+We could run this right away to test if it works, but while we're at it, we're also going to add a couple of [`view()`](https://www.nextflow.io/docs/latest/reference/operator.html#view) operators, which allow us to inspect the contents of a channel.
 You can think of `view()` as a debugging tool, like a `print()` statement in Python, or its equivalent in other languages.
 
 In the workflow block, make the following code change:
@@ -540,12 +540,25 @@ _After:_
 ```groovy title="hello-channels.nf" linenums="31"
     // create a channel for inputs
     greeting_ch = Channel.of(greetings_array)
-                         .view { "Before flatten: $it" }
+                         .view { greeting -> "Before flatten: $greeting" }
                          .flatten()
-                         .view { "After flatten: $it" }
+                         .view { greeting -> "After flatten: $greeting" }
 ```
 
-Here `$it` is an implicit variable that represents each individual item loaded in a channel.
+We are using an operator _closure_ here - the curly brackets.
+This code executes for each item in the channel.
+We define a temporary variable for the inner value, here called `greeting` (it could be anything).
+This variable is only used within the scope of that closure.
+
+In this example, `$greeting` represents each individual item loaded in a channel.
+
+!!! note "Note on `$it`"
+
+    In some pipelines you may see a special variable called `$it` used inside operator closures.
+    This is an _implicit_ variable that allows a short-hand access to the inner variable,
+    without needing to define it with a `->`.
+
+    We prefer to be explicit to aid code clarity, as such the `$it` syntax is discouraged and will slowly be phased out of the Nextflow language.
 
 #### 3.2.3. Run the workflow
 
@@ -723,9 +736,9 @@ _After:_
 ```groovy title="hello-channels.nf" linenums="31"
 // create a channel for inputs from a CSV file
 greeting_ch = Channel.fromPath(params.greeting)
-                     .view { "Before splitCsv: $it" }
+                     .view { csv -> "Before splitCsv: $csv" }
                      .splitCsv()
-                     .view { "After splitCsv: $it" }
+                     .view { csv -> "After splitCsv: $csv" }
 ```
 
 As you can see, we also include before/after view statements while we're at it.
@@ -787,7 +800,7 @@ This is what the syntax looks like:
 
 This means 'for each element in the channel, take the first of any items it contains'.
 
-So let's apply that to our CVS parsing.
+So let's apply that to our CSV parsing.
 
 #### 4.3.1. Apply `map()` to the channel
 
@@ -798,21 +811,21 @@ _Before:_
 ```groovy title="hello-channels.nf" linenums="31"
 // create a channel for inputs from a CSV file
 greeting_ch = Channel.fromPath(params.greeting)
-                     .view { "Before splitCsv: $it" }
+                     .view { csv -> "Before splitCsv: $csv" }
                      .splitCsv()
-                     .view { "After splitCsv: $it" }
+                     .view { csv -> "After splitCsv: $csv" }
 ```
 
 _After:_
 
 ```groovy title="hello-channels.nf" linenums="31"
 // create a channel for inputs from a CSV file
 greeting_ch = Channel.fromPath(params.greeting)
-                     .view { "Before splitCsv: $it" }
+                     .view { csv -> "Before splitCsv: $csv" }
                      .splitCsv()
-                     .view { "After splitCsv: $it" }
+                     .view { csv -> "After splitCsv: $csv" }
                      .map { item -> item[0] }
-                     .view { "After map: $it" }
+                     .view { csv -> "After map: $csv" }
 ```
 
 Once again we include another `view()` call to confirm that the operator does what we expect.

docs/hello_nextflow/03_hello_workflow.md

@@ -485,8 +485,8 @@ _After:_
     collectGreetings(convertToUpper.out.collect())
 
     // optional view statements
-    convertToUpper.out.view { "Before collect: $it" }
-    convertToUpper.out.collect().view { "After collect: $it" }
+    convertToUpper.out.view { greeting -> "Before collect: $greeting" }
+    convertToUpper.out.collect().view { greeting -> "After collect: $greeting" }
 }
 ```
 
@@ -816,11 +816,9 @@ _After:_
     collectGreetings(convertToUpper.out.collect(), params.batch)
 
     // emit a message about the size of the batch
-    collectGreetings.out.count.view { "There were $it greetings in this batch" }
+    collectGreetings.out.count.view { num_greetings -> "There were $num_greetings greetings in this batch" }
 ```
 
-Here we are using `$it` in the same way we did earlier, as an implicit variable to access the contents of the channel.
-
 !!! note
 
     There are a few other ways we could achieve a similar result, including some more elegant ones like the `count()` operator, but this allows us to show how to handle multiple outputs, which is what we care about.

docs/hello_nextflow/05_hello_containers.md

@@ -189,7 +189,7 @@ You can see that the filesystem inside the container is different from the files
     When you run a container, it is isolated from the host system by default.
     This means that the container can't access any files on the host system unless you explicitly allow it to do so.
 
-You will learn how to do that in a minute.
+    You will learn how to do that in a minute.
 
 #### 1.3.2. Run the desired tool command(s)
 
@@ -434,7 +434,7 @@ _Before:_
     collectGreetings(convertToUpper.out.collect(), params.batch)
 
     // emit a message about the size of the batch
-    collectGreetings.out.count.view{ "There were $it greetings in this batch" }
+    collectGreetings.out.count.view{ num_greetings -> "There were $num_greetings greetings in this batch" }
 ```
 
 _After:_
@@ -444,7 +444,7 @@ _After:_
     collectGreetings(convertToUpper.out.collect(), params.batch)
 
     // emit a message about the size of the batch
-    collectGreetings.out.count.view{ "There were $it greetings in this batch" }
+    collectGreetings.out.count.view{ num_greetings -> "There were $num_greetings greetings in this batch" }
 
     // generate ASCII art of the greetings with cowpy
     cowpy(collectGreetings.out.outfile, params.character)

docs/hello_nextflow/index.md

@@ -12,7 +12,7 @@ The rise of big data has made it increasingly necessary to be able to analyze an
 
 During this training, you will be introduced to Nextflow in a series of complementary hands-on workshops.
 
-Let's get started! Click on the "Open in GitHub Codespaces" button below.
+Let's get started! Click on the "Open in GitHub Codespaces" button below to launch the training environment (preferably in a separate tab), then read on while it loads.
 
 [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)