Add Scripting essentials module

[pinin4fjords]

Add Essential Nextflow Scripting Patterns side quest

This PR introduces a comprehensive hands-on tutorial that teaches essential Nextflow scripting patterns through practical bioinformatics examples.

Summary

The "Essential Nextflow Scripting Patterns" side quest takes learners on a journey from basic concepts to production-ready patterns, transforming a simple CSV-reading workflow into a sophisticated bioinformatics pipeline step-by-step.

Topics Covered

• Dataflow vs Scripting: Understanding the boundaries between workflow orchestration and data manipulation
• Data Manipulation: Working with maps and collections using operators like findAll(), collectEntries(), and groupBy()
• String Processing: Regex patterns for parsing complex file naming schemes and mastering variable interpolation
• Reusable Functions: Extracting complex logic into named functions for maintainable workflows
• Dynamic Logic: Building adaptive processes with closures for dynamic resource allocation
• Conditional Routing: Intelligent sample routing based on metadata characteristics
• Safe Operations: Null-safe operators and input validation with clear error messages
• Event Handlers: Configuration-based logging, notifications, and lifecycle management

Target Audience

Learners who have completed Hello Nextflow or have equivalent experience with basic Nextflow concepts (processes, channels, workflows). Programming experience is helpful but not required—concepts are explained as encountered.

Structure

The tutorial uses a realistic dataset (CSV with biological sample metadata) and evolves a working pipeline through practical challenges, building from fundamentals to advanced production patterns.

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[bentsherman]

I think this content is awesome, but I have a higher-level objection to the use of "Groovy" at all.

The Nextflow language specification was created in part to make it easier to talk about Nextflow as a standalone language. So rather than saying "Nextflow is based on Groovy but we promise it's not that bad!" we can instead say "Nextflow is a programming language that runs on the JVM".

It also gets confusing when talking about things like "Nextflow operators" vs "Groovy functions"... well, Nextflow operators are Groovy functions! They have the same syntax and (mostly) the same semantics

And it will get more confusing in 25.10 when it becomes possible to write code like this:

def sample_ids: List<String> = ['sample_001', 'sample_002', 'sample_003']

Which this tutorial might call "pure Groovy code", but isn't really pure Groovy because it isn't valid Groovy syntax. The distinction between Nextflow and Groovy will become less and less useful over time as the languages diverge futher

I think the distinction you are usually getting at with "Nextflow constructs" vs "Groovy constructs" is dataflow logic in the workflow vs "regular" logic (procedural logic?) in places like an operator closure. So I would describe it in those terms instead of Nextflow vs Groovy

Similarly, on the section about collect operator vs Groovy's collect method, well... this method is in the Nextflow standard library! So you don't even need to talk about Groovy, you can just say it's the collect method of the Iterable type vs the Channel type

In fact, I think you should be able to link any piece of syntax or standard library to the Nextflow reference docs -- and if you can't find it, tell me and I will add it. I want to have the Nextflow language fully specified within our docs so that we don't have to mention Groovy at all. I mean it

[pinin4fjords]

Thanks for the feedback @bentsherman, really useful. I'll re-pitch and get you to re-review if you get time.

Edit: done, with Claude's help.

I've used 'scripting' as the counterpoint to 'dataflow', because we're not necessarily talking to a crowd to whom 'procedural' makes enough sense. See what you think.

[bentsherman]

Left a few suggestions, fixed a few incorrect links.

Try to make sure to follow best practices with Nextflow code examples:

• Use channel instead of Channel for channel factories
• Avoid implicit it closure parameter
• Use tuple() instead of a list when you want to make a tuple

You might have to fight the AI on this since these patterns are historically quite common. Maybe just including the above guidance in your prompt will be enough 🤷

Thanks for putting all of this together. I intend to keep expanding the language reference docs to support these kinds of examples