1. Clone this repostiory to your home directory from vc7-shared

   cd ~
   git clone https://github.com/jemunro/wehi-nextflow-training.git
   

2. Create a run directory on /vast/

   mkdir -p /vast/scratch/users/$USER/nf-training-run
   

3. Change to the run directory

   cd /vast/scratch/users/$USER/nf-training-run
   

4. Load the nextflow module

   module load nextflow/22.04.5
   

5. Join the VSCode live share in your browser

A brief introduction to the Nextflow language

Core concepts for developing Nextflow workflows

An example pipeline calling SARS-Cov-2 variants using bwa, samtools, bcftools and then visualising with R

• Official Nextflow documentaion
• Official Nextflow Slack
• nf-core - community pipelines
• nf-core Slack
• Introduction to Bioinformatics workflows with Nextflow and nf-core - comprehensive Nextflow tutorial using DSL2
• Groovy Web Console - useful for testing Groovy/Java code fragments