Nextflow: My First Bioinformatics Pipeline!

👩🏻‍💻 couple of years ago, I was thrown into the world of bioinformatics while working at an informatics company. My task? Updating an existing bioinformatics pipeline by adding a few new tools. Sound simple? It wasn’t. But looking back, that challenge ended up being one of the most rewarding learning experiences I’ve had, especially because it introduced me to Nextflow—a workflow language that’s become popular in bioinformatics.

The Challenge: Updating a Pipeline

When I first started working on the pipeline, my task was pretty clear: I needed to add more tools. But that’s where things got tricky. To add anything, I first had to understand the pipeline as it was. I needed to figure out how it worked, how the tools were connected, and how to run it successfully. Once I had that down, I was ready to prepare the Linux commands for the new tool, integrate it into the pipeline, and test it.

Let me tell you, it wasn’t as simple as just adding a few lines of code. I ran into all sorts of errors that I had to debug, and at first, it felt like a huge mess. But honestly, that process of debugging and figuring things out on my own taught me a lot.

After spending quite some time working with Nextflow, I now feel confident enough to share a few tips on how to get started. Even if you're completely new to workflow languages, don’t worry—there’s a clear path forward.

Getting Started with Nextflow: My Step-by-Step Guide

If you're already familiar with workflow languages like Snakemake or WDL, picking up Nextflow might be easier, as some concepts will be familiar. However, if you're new to this, it might feel a bit overwhelming at first. So, here’s how I recommend getting started:

1.Leverage Free Training Resources

I can’t recommend this enough—Nextflow’s training materials are a goldmine. They might take a bit of time, but they’re totally worth it, especially if you’re just starting out.

• Nextflow for Newcomers: This is a super beginner-friendly resource that walks you through the basics.

• Fundamentals Training: Once you’ve got the basics down, dive into this. It’s more in-depth and will help you understand Nextflow’s syntax, processes, and how to structure a larger pipeline.

These resources will give you a solid foundation, and once you’re through them, you’ll feel a lot more comfortable with Nextflow.

2.Experiment with Existing Pipelines

Okay, here’s where things get fun. Instead of trying to write a whole pipeline from scratch, start by playing around with existing pipelines. The Nextflow community has a ton of ready-to-go workflows available on nf-core. These pipelines are great because they follow best practices, and you can easily modify them to suit your needs.

• Pick a Pipeline: Choose something that interests you. For me, it was transcriptomics—so I picked the nf-core/rnaseq pipeline. But if you’re into genomics or anything else, there’s most likely a pipeline for that. Take a look through the available pipelines on nf-core, and pick one to dive into.

• Run with Test Data: Each nf-core pipeline comes with test data. Start by running the pipeline with that. This will help you get familiar with how it works.

• Run with Custom Data: Once you’ve got the test data working, try it with any other data. You can download this from public databases like GEO or use your own data if you have it. Running a pipeline with other data will teach you how to handle things like creating a samplesheet (trust me, you might run into some problems here, but that’s part of the learning process).

💡 Check the issues section of the GitHub repo or the nf-core Slack channel if you run into problems. There’s a lot of great information shared by others who might have faced the same issues.

3.Modify the Pipeline

Once you’re comfortable running the pipeline, try modifying it. This is where the real learning happens. You can start by replacing an existing tool with one you prefer or by adding a new one.

For instance, let’s say you’re working with the nf-core rnaseq pipeline that uses Trim Galore for trimming. Try adding Trimmomatic instead and see how it goes.

Here’s how I approached it:

• Create a Local Module: Add the tool manually as a local module first. This will give you a good understanding of how things fit together.

• Install from nf-core Modules: Once you’re comfortable, try installing the tool from the nf-core module library.

• Remove a Tool: Try removing a tool from the pipeline. This might sound easy, but you’ll quickly learn that it’s not just about deleting a line of code. You have to look through multiple files and make sure you’re not leaving unnecessary dependencies behind.

4.Build Your Own Pipeline

Once you’ve played around with modifying existing ones, you’ll be ready to build your own pipeline from scratch. Don’t worry if it’s not perfect—just follow the Nextflow templates and keep experimenting.

A Few Final Thoughts

Learning Nextflow isn’t about rushing to build the most complex pipeline right away. Instead, it’s about gradually gaining confidence, experimenting with tools, and getting comfortable with the syntax and structure. Start small, build up your knowledge, and soon enough, you’ll be able to modify pipelines, add new tools, and even create your own from scratch.

And remember, don’t be afraid of making mistakes! Every error is a opportunity to learn something new.

If this guide helped you or you have any questions, feel free to drop a comment below. Let’s learn together!