1. Orientation¶

This workshop should be completed using the Nextflow Training Gitpod Environment.

1.1 Getting started¶

You will need to move into the troubleshoot folder.

You will need to copy and unzip the data required for this training.

Exercise

Use the following command to switch to the empty troubleshoot folder:

cd /workspace/gitpod/troubleshoot
cp -r /workspace/gitpod/hello-nextflow/data/ .
tar -zxvf data/ref.tar.gz -C data/

To check everything is working as expected you can run the hello-gatk.nf script located in the troubleshoot folder.

If all of the data has been copied and unzipped correctly you should see the pipeline execute three processes: