Merge branch 'master' into nf_test_genomics_test

Author: pinin4fjords

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)
 

docs/nf4_science/genomics/index.md

@@ -11,10 +11,9 @@ It builds on the [Hello Nextflow](../../hello_nextflow/) beginner training and d
 
 Specifically, this course demonstrates how to implement a simple variant calling pipeline with [GATK](https://gatk.broadinstitute.org/) (Genome Analysis Toolkit), a widely used software package for analyzing high-throughput sequencing data.
 
-!!! note
+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.
 
-    Don't worry if you're not familiar with GATK specifically.
-    We'll summarize the necessary concepts as we go, and the workflow implementation principles we demonstrate here apply broadly to any command line tool that processes genomics data.
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
 
 ## Learning objectives
 
@@ -40,9 +39,3 @@ The course assumes some minimal familiarity with the following:
 - Foundational Nextflow concepts and tooling covered in the [Hello Nextflow](../../hello_nextflow/) beginner training.
 
 For technical requirements and environment setup, see the [Environment Setup](../../envsetup/) mini-course.
-
-## Get started
-
-To get started, open the training environment by clicking the 'Open in GitHub Codespaces' button below.
-
-[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)

docs/nf4_science/rnaseq/00_orientation.md

@@ -3,7 +3,7 @@
 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.
+If you have not yet done so, please the [Environment Setup](../../envsetup/) mini-course before going any further.
 
 ## Materials provided
 

docs/nf4_science/rnaseq/index.md

@@ -11,18 +11,23 @@ It builds on the [Hello Nextflow](../../hello_nextflow/) beginner training and d
 
 Specifically, this course demonstrates how to implement a simple bulk RNAseq processing pipeline to trim adapter sequences, align the reads to a genome reference and performs quality control (QC) at several stages.
 
+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)
+
 ## Learning objectives
 
 By working through this course, you will learn how to apply foundational Nextflow concepts and tooling to a typical RNAseq use case.
 
 By the end of this workshop you will be able to:
 
 - Write a linear workflow to apply basic RNAseq processing and QC methods
-- Handle domain-specific files such as FastQ and reference genome resources appropriately
+- Handle domain-specific files such as FASTQ and reference genome resources appropriately
 - Handle single-end and paired-end sequencing data
 - Leverage Nextflow's dataflow paradigm to parallelize per-sample RNAseq processing
+- Aggregate QC reports across multiple steps and samples using relevant channel operators
+
 <!-- TODO
-- Implement **[quality control aggregation??]** using relevant channel operators
 - Configure pipeline execution and manage and optimize resource allocations
 - Implement per-step and end-to-end pipeline tests that handle RNAseq-specific idiosyncrasies appropriately
 -->
@@ -37,9 +42,3 @@ The course assumes some minimal familiarity with the following:
 - Foundational Nextflow concepts and tooling covered in the [Hello Nextflow](../../hello_nextflow/) beginner training.
 
 For technical requirements and environment setup, see the [Environment Setup](../../envsetup/) mini-course.
-
-## Get started
-
-To get started, open the training environment by clicking the 'Open in GitHub Codespaces' button below.
-
-[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)