Implementing scalable bioinformatics workflows in Snakemake and Nextflow

The Australian BioCommons / EMBL-ABR offers free, hands-on bioinformatics workshops around Australia. Registrations are now open for Implementing Scalable Bioinformatics Workflows in Snakemake & Nextflow.

OVERVIEW

Recent years have seen a groundswell of support in the bioscience community for improved reproducibility of data analyses. Large analysis workflows are fragile ecosystems of software tools, scripts and dependencies. One solution to these issues is the use of the workflow management systems such as Nextflow and Snakemake.

Trainees will be exposed to a common analytical pipeline, implemented in both Nextflow and Snakemake, which can be seamlessly executed across different computing environments (laptop/desktop to High Performance Computing). Trainees will be asked to extend these workflows and implement their own workflows from scratch. In doing so, this will facilitate the learning of core concepts of importance to both workflow managers, while also providing a means to compare and contrast the two.

The workshop will be presented in two parts by researchers who use these tools in their own work. Dr Radoslaw Suchecki is a Research Scientist at Agriculture and Food, CSIRO, and Dr Nathan Watson-Haigh is a Senior Bioinformatician at the Bioinformatics Hub, University of Adelaide.

LEARNING OUTCOMES

By completing this workshop, participants will be able to:

  • Execute existing Nextflow and Snakemake workflows
  • Understand the basic concept required for building a workflow from scratch
  • Implement a simple extension to an existing workflow
  • Learn how to scale workflows onto High Performance Computing (HPC) infrastructure
  • Understand the different paradigms underpinning Snakemake and Nextflow so a choice can be made about which to move forward with.

INTENDED AUDIENCE

This workshop is intended for researchers who use bioinformatics workflows in their research, but who do not yet have knowledge of Nextflow or Snakemake.

Prerequisites:

  • Experience with at least 1 scripting language
  • Experience with the Linux command line

FORMAT

Participants will meet at JCSMR (ANU) and connect with the lead trainer via an online interactive presentation. The training will comprise a series of short presentations combined with guided hands-on exercises on your own laptop. You will be supported by trained local facilitators and live online help from experienced bioinformaticians. Participants will need to attend both days of this two-part workshop: 12.00-4.00pm AEST on Wed 25th and Thu 26th September. Registration is essential and places are limited.

WHAT TO BRING

You will need an internet-enabled laptop.

Throughout the workshop you will be accessing a virtual Linux cluster in the cloud. Windows users will need to install PuTTY or Git Bash before attending. 

This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to EMBL-ABR News.

Date & time

12pm 25 September – 4pm 26 September 2019

Speakers

Radoslaw Suchecki, CSIRO
Nathan Watson-Haigh, University of Adelaide

Contacts

 Christina Hall

Updated:  21 September 2019/Responsible Officer:  Director/Page Contact:  Coordinator