Course Overview
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.
Intended Audience
Persons wishing to get familiar with and use Nextflow. Reference Graph and Containerization Hackathon participants needing to gain familiarity with Nextflow.
Keywords: Workflows, bioinformatics, reproducible
Skill level of training: Beginner
Language: English
Credential awarded: No credential awarded
Type of training: Online
Venue of the course:
Dates for the course: Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT
Course organisers: Phelelani Mpangase, Shaun Aron, Christopher Fields, Gerrit Botha, Suresh Maslamoney, Yasmina Jaufeerally Fakim, Shakuntala Baichoo, Itunuoluwa Isewon, Scott Hazelhurst, Sumir Panji, Nicky Mulder
Course Sponsors: Sydney Brenner Institute for Molecular Biology and H3ABioNet
Course objectives

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.

Classroom applications

Registration for classrooms opens: Thu, 01/01/1970
Registration for classrooms closes: Thu, 01/01/1970
Link to classroom application form:
Notification date for successful classrooms: Sun, 29/11/2020
Maximum number of participants that may be accepted per classroom will be capped at

Participant applications

Registration for participants opens: Wed, 25/11/2020
Registration for participants closes: Fri, 27/11/2020
Syllabus and Tools




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

Course limitations
This workshop will only provide a foundation for continued learning for using Nextflow to create bioinformatics workflows.
For more information, please visit
Training material 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.