Split hello_nextflow quiz into each chapter

Author: ewels

docs/hello_nextflow/01_hello_world.md

@@ -697,3 +697,95 @@ More generally, you know how to interpret a simple Nextflow workflow, manage its
 
 Take a little break, you've earned it!
 When you're ready, move on to Part 2 to learn how to use channels to feed inputs into your workflow, which will allow you to take advantage of Nextflow's built-in dataflow parallelism and other powerful features.
+
+## Quiz
+
+Test your knowledge of the concepts covered in Part 1 with this short quiz:
+
+!!! info
+
+    <!-- mkdocs-quiz intro -->
+
+<quiz>
+What is the minimum requirement for a Nextflow process?
+
+- [ ] Input and output blocks
+- [x] Output and script blocks
+- [ ] Only a script block
+- [ ] Input block
+
+</quiz>
+
+<quiz>
+What does the output block in a process do?
+
+- [ ] Creates the output files automatically
+- [x] Declares what output files to expect from the process
+- [ ] Determines the format of the output
+- [ ] Publishes outputs to a directory
+
+</quiz>
+
+<quiz>
+What command is used to run a Nextflow workflow?
+
+- [ ] `nextflow execute script.nf`
+- [x] `nextflow run script.nf`
+- [ ] `nextflow start script.nf`
+- [ ] `nextflow launch script.nf`
+
+</quiz>
+
+<quiz>
+What is stored in the `work/` directory?
+
+- [ ] Only the final output files
+- [ ] Configuration files
+- [x] Temporary files for each process execution
+- [x] Execution metadata like `.command.sh` and `.exitcode`
+- [x] Output files from processes
+- [ ] Container images
+
+</quiz>
+
+<quiz>
+What does the `-resume` flag do?
+
+- [ ] Restarts the entire workflow from scratch
+- [x] Skips processes that already ran with the same code, settings, and inputs
+- [ ] Resumes only failed processes
+- [ ] Saves the workflow state for later
+
+</quiz>
+
+<quiz>
+What is the default mode for the `publishDir` directive?
+
+- [ ] copy
+- [x] symlink
+- [ ] move
+- [ ] hardlink
+
+</quiz>
+
+<quiz>
+How do you pass a parameter to a Nextflow workflow from the command line?
+
+- [ ] `-parameter value`
+- [x] `--parameter value`
+- [ ] `params.parameter = value`
+- [ ] `-p parameter=value`
+
+</quiz>
+
+<quiz>
+Which quote type is required for variable interpolation in Nextflow?
+
+- [x] Double quotes `"`
+- [ ] Single quotes `'`
+- [ ] Backticks `` ` ``
+- [ ] Triple quotes `"""`
+
+</quiz>
+
+<!-- mkdocs-quiz results -->

docs/hello_nextflow/02_hello_channels.md

@@ -904,3 +904,93 @@ More generally, you have a basic understanding of how Nextflow uses **channels**
 
 Take a big break, you worked hard in this one!
 When you're ready, move on to Part 3 to learn how to add more steps and connect them together into a proper workflow.
+
+## Quiz
+
+Test your knowledge of the concepts covered in Part 2 with this short quiz:
+
+!!! info
+
+    <!-- mkdocs-quiz intro -->
+
+<quiz>
+What is a channel in Nextflow?
+
+- [ ] A file directory
+- [x] A queue-based mechanism for passing data between processes
+- [ ] A configuration parameter
+- [ ] A container registry
+
+</quiz>
+
+<quiz>
+Which channel factory creates a simple queue channel with values?
+
+- [ ] `channel.fromPath()`
+- [x] `channel.of()`
+- [ ] `channel.from()`
+- [ ] `channel.create()`
+
+</quiz>
+
+<quiz>
+What happens when you pass a channel with multiple values to a process?
+
+- [ ] Only the first value is processed
+- [x] The process is called once for each value in the channel
+- [ ] All values are processed together in a single call
+- [ ] The workflow fails with an error
+
+</quiz>
+
+<quiz>
+What does the `flatten()` operator do?
+
+- [x] Unpacks array contents into individual items
+- [ ] Removes duplicate items from a channel
+- [ ] Sorts channel contents alphabetically
+- [ ] Converts items to lowercase
+
+</quiz>
+
+<quiz>
+What is the purpose of the `view()` operator?
+
+- [ ] To visualize the workflow structure
+- [x] To inspect and print channel contents for debugging
+- [ ] To create graphical output
+- [ ] To validate channel data types
+
+</quiz>
+
+<quiz>
+What does the `splitCsv()` operator do?
+
+- [ ] Creates a CSV file from channel data
+- [x] Parses CSV-formatted content, reading each line into an array
+- [ ] Splits a channel into multiple channels
+- [ ] Validates CSV formatting
+
+</quiz>
+
+<quiz>
+Which operator transforms channel contents element-by-element?
+
+- [ ] `transform()`
+- [ ] `apply()`
+- [x] `map()`
+- [ ] `modify()`
+
+</quiz>
+
+<quiz>
+Why do you need dynamic filenames when processing multiple inputs?
+
+- [ ] To save disk space
+- [ ] To improve performance
+- [x] To prevent output files from overwriting each other
+- [ ] To make resume work correctly
+
+</quiz>
+
+<!-- mkdocs-quiz results -->

docs/hello_nextflow/03_hello_workflow.md

@@ -867,3 +867,83 @@ More generally, you understand the key principles involved in connecting process
 
 Take an extra long break, you've earned it.
 When you're ready, move on to Part 4 to learn how to modularize your code for better maintainability and code efficiency.
+
+## Quiz
+
+Test your knowledge of the concepts covered in Part 3 with this short quiz:
+
+!!! info
+
+    <!-- mkdocs-quiz intro -->
+
+<quiz>
+How do you access the output of a process in Nextflow?
+
+- [ ] `processName.output`
+- [x] `processName.out`
+- [ ] `processName.result`
+- [ ] `output.processName`
+
+</quiz>
+
+<quiz>
+What determines the execution order of processes in a workflow?
+
+- [ ] The order they are defined in the file
+- [ ] Alphabetical order by process name
+- [x] The dependencies between processes (output → input)
+- [ ] The order they are called in the workflow block
+
+</quiz>
+
+<quiz>
+What does the `collect()` operator do?
+
+- [ ] Unpacks arrays into individual items
+- [x] Packages many channel items into a single array element
+- [ ] Removes null values from a channel
+- [ ] Collects error messages
+
+</quiz>
+
+<quiz>
+When should you use the `collect()` operator?
+
+- [ ] Before processing items individually in parallel
+- [x] Before a process that needs all results at once
+- [ ] To speed up channel operations
+- [ ] When publishing outputs
+
+</quiz>
+
+<quiz>
+How do you access named outputs from a process?
+
+- [ ] `processName.out[outputname]`
+- [x] `processName.out.outputname`
+- [ ] `processName.outputname`
+- [ ] `output.processName.outputname`
+
+</quiz>
+
+<quiz>
+What is the syntax for naming a process output?
+
+- [x] `output: path "file.txt", emit: myoutput`
+- [ ] `output: path "file.txt", name: myoutput`
+- [ ] `output: path "file.txt" as myoutput`
+- [ ] `output: path "file.txt" -> myoutput`
+
+</quiz>
+
+<quiz>
+When passing multiple inputs to a process, what must match?
+
+- [x] The order of inputs in the workflow call must match the input block order
+- [ ] The data types must all be the same
+- [ ] The variable names must match exactly
+- [ ] The number of inputs must equal the number of outputs
+
+</quiz>
+
+<!-- mkdocs-quiz results -->

docs/hello_nextflow/04_hello_modules.md

@@ -382,3 +382,75 @@ This is better than just copy-pasting the code, because if later you decide to i
 
 Take a short break if you feel like it.
 When you're ready, move on to Part 5 to learn how to use containers to manage software dependencies more conveniently and reproducibly.
+
+## Quiz
+
+Test your knowledge of the concepts covered in Part 4 with this short quiz:
+
+!!! info
+
+    <!-- mkdocs-quiz intro -->
+
+<quiz>
+What is a Nextflow module?
+
+- [ ] A configuration file
+- [ ] A workflow definition
+- [x] A standalone file containing a single process definition
+- [ ] A container image
+
+</quiz>
+
+<quiz>
+What is the recommended filename convention for modules?
+
+- [ ] `module_processName.nf`
+- [x] `processName.nf`
+- [ ] `processName.module`
+- [ ] `processName_module.nf`
+
+</quiz>
+
+<quiz>
+Where should module files typically be stored?
+
+- [ ] In the root directory
+- [ ] In the `lib/` directory
+- [x] In the `modules/` directory
+- [ ] In the `processes/` directory
+
+</quiz>
+
+<quiz>
+What is the correct syntax to import a module?
+
+- [ ] `import { processName } from './modules/processName.nf'`
+- [x] `include { processName } from './modules/processName.nf'`
+- [ ] `require { processName } from './modules/processName.nf'`
+- [ ] `use { processName } from './modules/processName.nf'`
+
+</quiz>
+
+<quiz>
+What happens to resume functionality when you convert processes to modules?
+
+- [ ] Resume stops working
+- [ ] Resume only works for the main workflow
+- [x] Resume continues to work normally
+- [ ] Resume works but cache is reset
+
+</quiz>
+
+<quiz>
+What are key benefits of using modules?
+
+- [ ] Faster execution time
+- [ ] Reduced memory usage
+- [x] Reuse processes in multiple workflows without duplication
+- [x] Easier maintenance - improve module once, all workflows benefit
+- [x] Better code organization
+- [ ] Automatic parallelization
+
+</quiz>
+
+<!-- mkdocs-quiz results -->