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1. Orientation

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


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

1.1 Getting started

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

In this folder you will find three pairs of zipped fastq files (*.fastq.gz) in a data/ folder and an example samplesheet (samplesheet.csv) in a scripts/ folder.

├── data
│   ├── gut_1.fastq.gz
│   ├── gut_2.fastq.gz
│   ├── liver_1.fastq.gz
│   ├── liver_2.fastq.gz
│   ├── lung_1.fastq.gz
│   └── lung_2.fastq.gz
└── scripts
    └── samplesheet.csv

Each file will be used in this training module.


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-customize
tree .

Congratulations! You are now ready to start the workshop!