This tutorial aims to get you familiarized with Nextflow. After this course you should be able to understand workflow pipelines that are written in Nextflow and write simple pipelines yourself! Here’s an overview of the materials that we will cover:

  • General introduction to Nextflow

  • Building blocks of Nextflow: processes, channels and operators, workflows and modules

  • Executing pipelines

  • Creating our first Nextflow script(s)

  • Managing configurations: parameters, portability, executors

The course materials are focused on the newer version of Nextflow DSL2. This is the newest version of the Nextflow language and the de-facto standard for writing new pipelines in Nextflow. In fact, DSL1 is supposed to be fading out and chances are that the support for DSL1 will be gone within a near future. Must you have any questions regarding pipelines written in DSL1, feel free to ask any questions during the workshop.

References and further reading#

Here are some great tips for learning and to get inspired for writing your own pipelines:

  • Nextflow’s official documentation (link)

  • Reach out to the community on Slack (link)

  • Curated collection of patterns (link)

  • Workshop focused on DSL2 developed by CRG Bioinformatics Core (link)

  • Tutorial exercises (DSL1) developed by Seqera (link)

  • Curated ready-to-use analysis pipelines by NF-core (link)

  • Model example pipeline on Variant Calling Analysis with NGS RNA-Seq data developed by CRG (link)

  • Tutorial by Andrew Severin (link)

  • Nextflow community basic training (link)