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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 workflows.

We will start by discussing the core features of nf-core and Nextflow and learning the fundamental commands and options for executing workflows. This knowledge will be applied as we learn about the structure of nf-core workflows and how to customize their execution. Finally we start working on a real-life nf-core workflow - 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 workflow to optimise it for our data and computing environment.

1.0.1 Create a new work directory

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

Create a new working directory

Start by creating a new directory for all of today's activities:

mkdir ~/session1

Once created, open the folder in VS Code:

  1. Use the keyboard shortcut Ctrl + O (Windows/Linux) or Cmd + O (MacOS).
  2. Navigate to /home/<USERNAME>/session1 and click "Open" or press Enter, replacing <USERNAME> with your provided user name. The screen will refresh and the active folder in your VS Code session will now be the session1 folder.

Tip

You can also open files and folders in VS Code using the code command we installed during setup:

code ~/session1

Remember: <USERNAME> is a placeholder

At the start of this workshop, you will have a unique user name provided to you. Throughout these materials, we will use <USERNAME> as a placeholder, which you will need to replace with the user name given to you.