Course Overview/Description: The use of workflow technologies such as Nextflow is becoming increasingly pervasive in bioinformatics. Workflows automate the execution of various bioinformatics tools and pipelines and reduces the time one spends on running the different steps in a particular pipeline while testing various parameters as well as enabling reproducible analysis. The “Introduction to Nextflow” workshop will provide an introduction to workflows, some basic usage and syntax for using Nextflow.

Keywords: Workflows, bioinformatics, reproducible

Skill level of training: Beginner

Language: English

Credential awarded: None

Type of training: Online training

Venue of workshop: Virtual

Dates for the workshop (duration if run as a MOOC): 1st December 2020 – 2:30pm CAT

Workshop organisers: Phelelani Mpangase, Shaun Aron, Christopher Fields, Gerrit Botha, Suresh Maslamoney, Yasmina Jaufeerally Fakim, Shakuntala Baichoo, Itunuoluwa Isewon, Scott Hazelhurst, Sumir Panji, Nicky Mulder

Registration opens: 25th November 2020

Registration closes: 27th November 2020 at 10 pm CAT

Notification date: 29th November 2020

Link to application form:

Workshop Sponsors: Sydney Brenner Institute for Molecular Biology and H3ABioNet

Intended Audience: Persons wishing to get familiar with and use Nextflow. Reference Graph and Containerization Hackathon participants needing to gain familiarity with Nextflow.

Syllabus and Tools:

  • Introduction to Nextflow
  • Use of workflow systems for automation / reproducibility
  • Basic syntax of Nextflow
  • Transform and execute a workflow in Nextflow

Licensing for course materials: Creative commons


Learning objectives/outcomes: After this workshop participants should be able to:

  • Find and use Nextflow tool definitions online.
  • Understand how to write Nextflow scripts and definitions for command line tools.
  • Understand the concepts of Nextflow Channels, Processes and Channel operators.
  • Understand how to handle multiple inputs and outputs in Nextflow.
  • Understand Nextflow's configuration file (nextflow.config), profiles and input parameters.
  • Use Docker/Singularity with Nextflow to provide software dependencies and ensure reproducibility.
  • Join Nextflow tools into a workflow.
  • Run Nextflow workflows on local, HPC and cloud systems.

 Workshop limitations: This workshop will only provide a foundation for continued learning for using Nextflow to create bioinformatics workflows.

 Workshop Programme: 




1 December 2020

14:00 – 15:00

Introduction to Nextflow

Phelelani Mpangase

15:00 – 15:30

Parameters, Channels and Processes


Phelelani Mpangase

15:30 – 16:00


Phelelani Mpangase

16:00 – 16: 30


Phelelani Mpangase

16:30 – 17:00

Channel Operations

Phelelani Mpangase

 Training Materials Availability:

Training materials for this course are available as a single downloadable archive here: Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.