2.0. Introduction to session 2

This session builds on fundamental concepts learned in Session 1 and provides you with hands-on experience in nf-core workflow customisation. Throughout the session we will be working with data from a published RNAseq study and the nf-core/rnaseq pipeline.

We will explore the pipeline source code and apply various customisations using a parameter file and custom configuration files. You will:

• Create these files for our case study
• Use the nf-core tools utility
• Run Nextflow commands to query work directories and configuration files
• Write some custom Bash code to efficiently extract information from the source code

Each lesson in this session will build on the previous lessons, so you can gain a deeper understanding of the customisation techniques and the impact they have on the workflow and your results 🤓

Applying what you learn here to other nf-core workflows

While all activities in this session will be performed using the nf-core/rnaseq workflow, all customisation scenarios we explore are applicable to other nf-core workflows and do not require an understanding of RNAseq data processing.

2.0.1. Log back in to your instance

Follow set up instructions to log back into your instance in either VS Code or your terminal.

In VS Code:

1. Type Ctrl + Shift + P to open command palette and select Remote-SSH: Connect to Host and nfcoreWorkshop
2. Type in your provided password (see the Slack channel for the password) and hit enter

OR

In a terminal application:

1. Type the following into your terminal, using your allocated instance’s IP address:

ssh training@146.118.XXX.XX

2. Type in your provided password (see the Slack channel for the password) and hit enter

2.0.2. Create a new work directory

Create a new directory for all session 2 activities and move into it:

mkdir ~/session2 && cd $_

All materials copyright Sydney Informatics Hub, University of Sydney