1. Orientation¶

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

Note

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

1.1 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.

1.2 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

Exercise

Open the Gitpod 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 /workspace/gitpod/nf-training
tree .

1.3 Environment variables¶

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.

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

export NXF_VER=23.10.1

Note

This tutorial workshop requires NXF_VER=23.10.1, or later.

If you have exported the NXF_VER variable, execute nextflow -version again to confirm that the change has taken effect.