Orientation

The GitHub Codespaces environment contains some test data that will be used in this workshop.

Note

Follow this link if you have not yet setup your GitHub Codespaces environment.

Getting started

You will complete this module in the nf-training/ folder.

In this folder you will find a series of data files (ggal, index, meta...) and several script and configuration files.

.
├── data
│   ├── ggal
│   │   └── <data files>
│   ├── index
│   │   └── <data files>
│   ├── meta
│   │   └── <data files>
│   ├── prots
│   │   └── <data files>
│   ├── reads
│   │   └── <data files>
│   └── test
│       └── <data files>
├── env.yml
├── hello.nf
├── hello_py.nf
├── modules.hello.nf
├── nextflow.config
├── script1.nf
├── script2.nf
├── script3.nf
├── script4.nf
├── script5.nf
├── script6.nf
├── script7.nf
└── snippet.nf

Each file will be used in this training module.

Selecting a Nextflow version

By default, Nextflow will pull the latest stable version into your environment.

However, Nextflow is constantly evolving as improvements are made.

The latest releases can be viewed on GitHub here.

If you want to use a specific version of Nextflow, you can set the NXF_VER variable as shown below:

export NXF_VER=23.10.1

You can double-check NXF_VER by running:

nextflow -version

Exercise

Open the GitHub Codespaces training environment and use the following command to switch to the nf-customize folder. View the files in this folder using the tree command:

cd /workspaces/training/nf-training
tree .