Orientation¶

GitHub Codespaces¶

The GitHub Codespaces 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) GitHub 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 go through the Environment Setup mini-course before going any further.

Warning

This training is designed for nf-core tools version 3.4.1, which should be the version installed in the codespace. If you use a different version of nf-core tooling you may have difficulty following along.

You can check what version is installed using the commandnf-core --version.

Working directory¶

Throughout this training course, we'll be working in the hello-nf-core/ directory.

Change directory now by running this command in the terminal:

cd hello-nf-core/

Tip

If for whatever reason you move out of this directory, you can always use the full path to return to it, assuming you're running this within the Github Codespaces training environment:

cd /workspaces/training/hello-nf-core

Now let's have a look at the contents of this directory.

What you'll learn¶

This training course teaches you the core concepts for building nf-core-style pipelines. We can't cover everything—nf-core pipelines have many features and conventions developed by the community over years—but we focus on the essential concepts that will help you get started and understand how nf-core works.

First, you'll run an existing nf-core pipeline to understand how they're structured and what makes them different from basic Nextflow workflows. The extensive directory structure, configuration system, and standardized conventions might seem overwhelming at first, but understanding them is essential for working within the template.

Next, you'll adapt a simple workflow to the nf-core template scaffold. Most real pipelines start from existing code, so learning how to restructure workflows to work within nf-core's nested workflow system is a practical skill you'll use repeatedly.

Then you'll discover one of nf-core's biggest advantages: the community modules library. Instead of writing every process from scratch, you'll learn to integrate pre-built, tested modules that wrap common bioinformatics tools. This approach saves time and ensures consistency across pipelines.

Of course, the modules library doesn't have everything, so you'll create your own nf-core-style module. You'll learn the specific structure, naming conventions, and metadata requirements that make modules shareable and maintainable by the community.

Finally, you'll implement comprehensive validation for both command-line parameters and input data files using nf-schema. This catches errors before pipelines run, providing fast feedback and clear error messages—a key differentiator between research scripts and production pipelines.

By the end, you'll have transformed a basic Nextflow workflow into a production-ready, nf-core-style pipeline with standardized structure, reusable components, and robust validation.

Materials provided¶

You can explore the contents of this directory by using the file explorer on the left-hand side of the training workspace. Alternatively, you can use the tree command.

Throughout the course, we use the output of tree to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity.

Here we generate a table of contents to the second level down:

tree . -L 2

If you run this inside hello-nf-core, you should see the following output:

Directory contents

.
├── greetings.csv
├── original-hello
│   ├── hello.nf
│   ├── modules
│   └── nextflow.config
└── solutions
    ├── composable-hello
    ├── core-hello-part2
    ├── core-hello-part3
    ├── core-hello-part4
    └── core-hello-start

8 directories, 3 files

Here's a summary of what you should know to get started:

The greetings.csv file is a CSV containing some minimal columnar data we use for testing purposes.
The original-hello directory contains a copy of the source code produced by working through the complete Hello Nextflow training series (with Docker enabled).
The solutions directory contains the completed workflow scripts that result from each step of the course. They are intended to be used as a reference to check your work and troubleshoot any issues.

Now, to begin the course, click on the arrow in the bottom right corner of this page.