Overview

The tutorial will be conducted both locally and on Lugh. The goal of this weeks tutorial is to get you comfortable designing your own containers, which play a huge role in creating reproducible workflows. This is the only week we will dedicate to creating containers, due to time constraints I will prepare containers for subsequent weeks analyses.

We will cover the following topics:

1. Conda: Install packages & create environments using a yaml file ~20 min
2. Docker: Create Image using Dockerfile with a Conda layer. Push image to Dockerhub ~20 min
3. Singularity: Pull image from Dockerhub and convert to container ~20 min
4. Nextflow: Create workflow pipeline performing QC on sequencing reads ~1 hour

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Prerequisites

Please make sure you have the following for the tutorial:

• Local Anaconda installation.
• Local Docker installation.
• Please create a Docker hub account.
• Local Singularity installation.
• Local Nextflowinstallation.

Note: the above hyperlinks are for ubuntu installation where applicable.