README.md

WEHI Nextflow Training

Prerequisites

• To complete the training, you will require an appropriate IDE/editor installed on your computer.
• Visual Studio Code is recommended, but for other options see https://nf-co.re/developers/editor_plugins.
• You will be editing code stored in your unix home directory through a WEHI NAS connection, see how to connect to NAS.

If using Visual Studio Code, the following extensions should be installed:

• https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow
• https://marketplace.visualstudio.com/items?itemName=ms-vsliveshare.vsliveshare
• https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh
  • Using this extension is a good alternative to using NAS to edit remote files. You can connect using vc7-shared as the remote host, for more details see remote coding with Visual Studio

Setup (on the day)

1. Open a termnial and SSH into vc7-shared
2. Clone this repostiory to your home directory

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

3. Create and navigate to a run directory on your vast scratch space

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

4. (Optional) start an interactive slurm session

   salloc --partition interactive --mem 8G --cpus-per-task 4 --time 2:00:00
   

5. Load the nextflow module

   module load nextflow/22.04.5
   

Module 1: Hello World

A brief introduction to the Nextflow language.

Module 2: Processes and Software Dependencies

Configuration of processes and software dependencies using an example RNA-seq pipeline.

Module 3: Nextflow Scripting

Scripting with Groovy and Nextflow. Creating channels and using operators.

Module 4: NGS Variant Calling Pipeline

Work though an example pipeline calling SARS-Cov-2 variants using bwa, samtools, bcftools and then visualising with R.

Using Nextflow on Milton

• Use screen or tmux to leave Nextflow pipelines running on vc7-shared
• Alternatively, submit pipelines to the long slurm partition
• Be aware of the VAST scratch deletion policy, make sure to transfer pipeline outputs to permanent storage

Additional Resources

Documentation

• Nextflow documentaion

Training

• Seqera Nextflow Training

Community Nextflow Pipelines

• nf-core

Getting Help

• Nextflow GitHub Discussions
• Nextflow Slack
• nf-core Slack