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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-develop folder.

This is an empty directory where you will create an launch your pipeline.


Open the Gitpod training environment and use the following command to switch to the empty nf-develop folder:

cd /workspace/gitpod/nf-develop

1.2 Configuring GitHub

As a part of this workshop you will push changes to your GitHub.

If this is the first time you have used Gitpod for development work you will need to edit your permissions to push changes.

To edit your Gitpod permissions, open your Gitpod dashboard by clicking on the three horizontal lines in the top left-hand corner of your browser window and select Gitpod: Open Dashboard from the dropdown menu.

Open Gitpod dashboard

In your dashboard, click on your avatar in the top right-hand corner of your window and select User Settings from the dropdown menu.

Gitpod dashboard

Click on Git Providers on the right hand menu.

Git providers

Edit the permissions for your GitHub account by clicking on the three dots next to your GitHub account and give your Gitpod account permissions to access for GitHub repositories.

GitHub permissions

Once complete, click Update permissions and return reopen your Gitpod training environment.

Congratulations! You are now ready to start the workshop!