Chapter 1 Introduction

Welcome to this short tutorial on Nextflow. We are going to walk through some of the functionalities of this powerful workflow engine. More specifically we are going to do some hands-on work on processes, channels and operators. We are also going to look into how to configure Nextflow to run on different platforms. But before moving forward, we need to set up the environment for using Nextflow.

1.1 Setting up the environment

We are going to use UPPMAX for doing most of the hands-on work.

First ssh to UPPMAX

ssh -AX youusername@rackham.uppmax.uu.se

Start an interactive uppmax session

interactive -A uppmax2024-2-11 -M snowy -t 02:00:00

Make a directory in your user space (only if you have not done before)

mkdir -p /crex/proj/uppmax2024-2-11/nobackup/$USER/nextflow_lab1

Navigate to the folder you have created

cd /crex/proj/uppmax2024-2-11/nobackup/$USER/nextflow_lab1

Load Nexflow

module load bioinfo-tools
module load Nextflow/22.10.1

If because of any reason, you cannot use UPPMAX, Nextflow can be installed on any POSIX compatible system for example Linux, OS X, Windows Subsystem for Linux. Head to Nextflow website and follow the installation procedure.