1. 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.

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

These files will be used in this training module.

Exercise

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

cd /workspaces/training/nf-customize
tree .

Congratulations! You are now ready to start the workshop!