Preface

This workshop aims at introducing you to the world of workflow managers, in particular the workflow manager Nextflow. This workshop was written as a practical for the EMBL-EBI predoc course, 2022 cohort. I hope that you will find it useful, and in any case, I would be happy to hear your feedback on it. You can contact me at saul@ebi.ac.uk.

The workshop is written with an increasing level of difficulty, so feel free to skip what is too easy for you or stop when things become too complex. The introduction section will help you set up all the software needed to follow this workshop. The basic features section will walk you through the fundamental concepts behind workflow managers in general and Nextflow in particular. The advanced features section will explore some more complex features of Nextflow. The basic challenge and the advanced challenge sections contain challenges for you to solve, at different levels of complexity.

This workshop does not aim at being complete in describing Nextflow functionality. If this is what you are looking for the best place to explore is the Nextflow documentation. My objective in writing this workshop is to present the features of Nextflow that I consider most important to know, and to give them in a way that shows you how you can use them in real-world scenarios. As for many topics in coding, there is not a single way for achieving the result that you want. Here I am showing you my way of writing Nextflow workflows. Many different approaches would be equally valid, and I encourage you to explore what works best for you and develop your own coding style.