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Getting started

Start a training environment

To use the pre-built environment we provide on GitHub Codespaces, click the "Open in GitHub Codespaces" button below. For other options, see Environment options.

We recommend opening the training environment in a new browser tab or window (use right-click, ctrl-click or cmd-click depending on your equipment) so that you can read on while the environment loads. You will need to keep these instructions open in parallel to work through the course.

Open in GitHub Codespaces

Environment basics

This training environment contains all the software, code and data necessary to work through the training course, so you don't need to install anything yourself.

The codespace is set up with a VSCode interface, which includes a filesystem explorer, a code editor and a terminal shell. All instructions given during the course (e.g. 'open the file', 'edit the code' or 'run this command') refer to those three parts of the VScode interface unless otherwise specified.

If you are working through this course by yourself, please acquaint yourself with the environment basics for further details.

Version requirements

This training works with Nextflow 25.10.2 or later with the v2 syntax parser, which is the default from Nextflow 26.04 onward. In our training environment you don't need to do anything: it runs Nextflow 26.04.4 with the v2 parser. If you are using a local or custom environment, see the version notes.

The pipelines in this course require Nextflow 25.10.4 or later

The nf-core/demo, nf-core/rnaseq and nf-core/fetchngs pipelines used in this course enforce their own minimum Nextflow version (>=25.10.4), which is stricter than the general training floor of 25.10.2. Our training environment already satisfies this; if you are using a local or custom environment, make sure you are on Nextflow 25.10.4 or later.

v2 parser compatibility

Many nf-core pipelines do not yet support the v2 syntax parser. If you run an nf-core pipeline other than those used in this course and encounter errors, you may need to switch to the v1 parser by setting export NXF_SYNTAX_PARSER=v1. See the version notes for details.

Get ready to work

Once your codespace is running, there are two things you need to do before diving into the training: set your working directory for this specific course, and take a look at the materials provided.

Set the working directory

By default, the codespace opens with the work directory set at the root of all training courses, but for this course, we'll be working in the nfcore-use/ directory.

Change directory now by running this command in the terminal:

cd nfcore-use/

If for whatever reason you move out of this directory (e.g. your codespace goes to sleep), 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/nfcore-use

Next, explore the contents of this directory.

Explore the 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.

tree .
Directory contents 
.
├── broken_samplesheet_1.csv
├── broken_samplesheet_2.csv
├── custom.config
├── data
│   ├── reads
│   │   ├── KO_1_S3_L001_R1_001.fastq.gz
│   │   ├── KO_1_S3_L001_R2_001.fastq.gz
│   │   ├── KO_2_S4_L001_R1_001.fastq.gz
│   │   ├── KO_2_S4_L001_R2_001.fastq.gz
│   │   ├── WT_1_S1_L001_R1_001.fastq.gz
│   │   ├── WT_1_S1_L001_R2_001.fastq.gz
│   │   ├── WT_1_S1_L002_R1_001.fastq.gz
│   │   ├── WT_1_S1_L002_R2_001.fastq.gz
│   │   ├── WT_2_S2_L001_R1_001.fastq.gz
│   │   └── WT_2_S2_L001_R2_001.fastq.gz
│   └── sra_ids.csv
├── INSTRUCTORS.md
├── laptop.config
├── malformed_samplesheet.csv
├── my_params.yml
└── solutions
    ├── samplesheet.csv
    └── tuned.config

3 directories, 20 files
  • The laptop.config file is a configuration file we'll use in Parts 3 and 5 to cap resource usage when running a production-scale pipeline locally. You can ignore it until then.
  • The my_params.yml, malformed_samplesheet.csv, and custom.config files are used in Part 2, to demonstrate setting parameters from a file, input validation, and process-level configuration overrides. You can ignore them until then too.
  • The data/reads/ directory contains FASTQ files for a small RNA-seq experiment, and the data/sra_ids.csv file lists public sequencing runs; both are used in Part 5 to prepare samplesheets.
  • The broken_samplesheet_1.csv and broken_samplesheet_2.csv files contain errors to diagnose and fix in Part 5.
  • The solutions/ directory contains the completed samplesheet from Part 5 and the tuned configuration file from Part 6.
  • The INSTRUCTORS.md file contains notes for instructors running the course live; you can ignore it.

Readiness checklist

Think you're ready to dive in?

  • I understand the goal of this course and its prerequisites
  • My environment is up and running
  • I've set my working directory appropriately

If you can check all the boxes, you're good to go.

To continue to Part 1, click on the arrow in the bottom right corner of this page.