nextflow_tutorial

The GitPod comes with Nextflow, Conda and Docker pre-installed

Once the pod launches, it will present a VS-Code interface

To create varcal environment based on yml file

mamba env update -n base -f environment.yml

To download reference genome and raw reads

bash data/fetch_raw_data.sh

To trim the reads using trimmomatic

bash data/trim.sh

Click here for Nextflow Tutorial - Variant Calling Edition tutorial