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1.0 Introduction to Session 1

During Session 1 we will establish fundamental ideas and skills that are essential for using Nextflow and customizing the execution of nf-core pipelines.

We will start by discussing the core features of nf-core and Nextflow and learning the fundamental commands and options for executing pipelines. This knowledge will be applied as we learn about the structure of nf-core pipelines and how to customize their execution. Finally we start working on a real-life nf-core pipeline - nf-core/rnaseq - and write a command to get it up and running.

The ideas and skills you learn during Session 1 will be applied during Session 2 where we will customise the execution of the nf-core/rnaseq pipeline to optimise it for our data and computing environment.

1.0.1 Create a new working directory

It is good practice to organize projects into their own folders to make it easier to track and replicate experiments over time.

Exercise 1.0.1 ⏱ 3 min

First, ensure you have followed all of the setup instructions and logged into your VM.

Create a new directory for all of today's activities:

mkdir ~/session1

Once created, open the folder in VS Code:

  1. Go to the File menu and select Open Folder....
  2. In the pop-up box, navigate to ~/session1 and click "Open" or press Enter. The screen will refresh and the active folder in your VS Code session will now be the session1 folder.