Who is this course for?

This course has now been archived. Up to date training is available at https://training.nextflow.io/ which hosts the community training material. 

The Seqera community team records a new set of videos walking through this material every 6 months as it's always evolving. These are shared freely on YouTube. 

This tutorial is for anyone who would like to start using Nextflow for their workflows. 

The videos and training materials used in this online tutorial were developed and presented by Seqera Labs. The content is made available under a CC BY-NC-ND licence by Seqera Labs.

The online version of this tutorial was developed as part of the EOSC-Life project; EOSC-Life has received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087.

What will I achieve?

By the end of the course you will be able to:

• Describe what Nextflow is used for
• Implement a workflow using Nextflow
• Recall how to deploy a Nextflow workflow

What resources do I need?

There are no specific resources required to watch the videos in this course.

To complete the tutorial described in the videos, it is recommended to use Gitpod (see section 1.2), as this is a closed environment with all the programs and data installed.

Local installation

Nextflow can be used on any POSIX compatible system (Linux, OS X, Windows Subsystem for Linux etc.).

Requirements:

• Bash
• Java 8 (or later, up to 15)
• Git

Optional requirements for this tutorial:

• Docker engine 1.10.x (or later)
• Singularity 2.5.x (or later)
• Conda 4.5 (or later)
• Graphviz
• AWS CLI
• AWS Batch computing environment configured

DOI: 10.6019/TOL.NextFlow-t.2022.00001.1

Course contents

How and when to access the course

All our courses are designed with flexibility in mind. You can access them for free at any time, just click on the "Enter Course" button.

It is up to you how you use the course; you can either study the full course or you can focus on sections that are relevant to you. To jump between sections, use the navigation bar on the left or the arrows at the bottom of the page. You can also choose whether to complete the course in one go, or over several visits.

The average time to read through the main body of the course is 3 hours (not including exercises and external links). The time may vary depending on your prior knowledge and how you choose to work through the course.

Sign up to track your learning and more

You can track your progress and keep a record of any completed learning by creating an account. This will give you a 'My learning' page, which will have three main tabs to help keep track of your progress:

Favourite: To add online tutorials to your Favourite tab, you can 'Mark as Favourite' on the front page of online tutorials, allowing you to return and complete them in the future.

In progress: The courses which you have started reading will be added to your 'In progress' tab. Use the 'Mark as complete' button at the end of the course pages to get started.Your ‘In progress’ tab gets updated as you progress through the course and will show you what percentage of the course you have finished and will let you resume the course from where you left on your last visit.

Completed: The courses which you have finished entirely will be added to the 'Completed' tab.

The results you gain from completing quizzes and other interactive content will also be added to your My learning page.

You can register anytime here or click a 'Favourite' or 'Mark as complete' button to start tracking your progress.

You can still access all the online tutorials and interactive content if you do not register, but you will not be able to track your progress.

Making the most of the course

Learning something new takes time and practice. We encourage you to:

• Use the activities and quizzes to help you check your learning, recall and apply key concepts. Look out for these icons 

• Revisit sections as and when you need them. Bookmark relevant pages in your browser or use the navigation panel to jump the relevant section.

Getting help and providing feedback

If something isn’t working or if you have a question get in touch by contacting us at trainonline@ebi.ac.uk

Tell us what you thought about the course (both good and bad!) using the “Feedback and help” button found at the top of each page.

Your feedback helps us ensure we are providing training that is relevant and useful for you.

For help and support on EMBL-EBI resources you can contact the helpdesk directly.

Learn more

You can explore other training on offer from EMBL-EBI on our website. We offer online courses, webinars, face-to-face courses and offsite training.