Introduction to Nextflow Workshop 2020

    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: https://redcap.h3abionet.org/redcap/surveys/?s=RDMT38HXMH

    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

    Prerequisites:

    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: 

    Time

    Topic

    Trainer

    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

    Docker/Singularity

    Phelelani Mpangase

    16:00 – 16: 30

    Executors

    Phelelani Mpangase

    16:30 – 17:00

    Channel Operations

    Phelelani Mpangase

     


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