Nextflow Workshop Prerequisites

Author

Affiliation

Seth Weaver

Bioinformatics Research Center

This page outlines what you should set up and review before the Nextflow workshop begins. Complete these steps ahead of time and review any materials necessary so you can come to the workshop ready to make the most of your time learing Nextflow!

1 Accessing the Hazel HPC

• Please verify that you have a Hazel HPC account and request one from your PI if you don’t yet have one

• Familiarize yourself with logging onto to Hazel via SSH:

SSH <unity_id>@login.hpc.ncsu.edu

For more information, review Getting Started on Hazel.

2 Command Line Familiarity

• You should have familiarity with navigating a Linux HPC environment and have a basic understanding of Hazel’s storage spaces. For more information and a Linux crash course using Hazel, see Tour of Hazel / Command Line 101.

3 Software and Modules

• The Nextflow pipelines you will be writing will use software containers hosted by the BRC. Please review the following documentation to learn more about how to use the BRC software repository: Using Shared Software on Hazel.

4 Interactive Jobs

• In order to work on and run pipelines in a compute-ready environement, we will be using interactive jobs using Slurm on Hazel. To request an interactive node:

# Requesting an interactive CPU node for XX hrs with XX cores and XX Gb of memory
srun --pty --time=XX:00:00 --cpus-per-task=XX --mem=XX bash

For more information about submitting jobs on Hazel, including interactive jobs, see Running Jobs with SLURM.

5 Github on Hazel

• The material for this course exists as a github repo, that you should download before hand. To clone a github repo run the following from your scratch directory:

git clone https://github.com/hurwitzlab/nextflow_crash_course.git

git is automatically set up on hazel, and you can clone repos over https without being logged in. To integrate github more completely, see Git and github on Hazel.

6 Understanding $PATH variables

Your path variable ($PATH) is a list of directorys that your system will automatically search for executable files (Usually /usr/local/bin, and /usr/bin, and /bin by default). If you are trying to execute a file not in one of those directories, you will need to provide an absolute or relative path to your file.

Additionally, you may add a new directory to your path with:

export PATH="$PATH:/path/to/your/directory"

7 Nextflow Background (Optional)

• Skim the Nextflow documentation for a general orientation

8 nf-core background (Optional)

• Learn more about the nf-core project, a community-driven initiative to right reproducible bioinformatics pipelines using Nextflow. All of these pipelines are available for you to run on Hazel! See Using nf-core pipelines for more information.