Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud
Channel: Australian BioCommons
Date: 2022-09-20

Bioinformatics workflows can support portable, reproducible and scalable analysis of omics datasets but using workflows can be challenging for both beginners and experienced bioinformaticians. Beginners face a steep learning curve to be able to build and deploy their own bioinformatics workflows while those with more experience face challenges productionising and scaling code for custom workflows and big data. 

Bioinformaticians across the world are using Nextflow to build and manage workflows. Many of these workflows are shared for others to use and supported by the community via nf-co.re. So far, 39 workflows for omics data are available with another 23 under development. These workflows cover common analyses such as RNAseq, mapping, variant calling, single cell transcriptomics and more and can be easily deployed by anyone, regardless of skill level.

In this webinar, Nandan Deshpande from the Sydney Informatics Hub, University of Sydney, will discuss how you can deploy freely available Nextflow (nf.co-re) bioinformatics workflows with a single command. We describe how you can quickly get started deploying these workflows using Pawsey Nimbus Cloud. For advanced users, we introduce you to Nextflow concepts to get you started with building your own workflows that will save you time and support reproducible, portable and scalable analysis.

In the latter half of the webinar, Sarah Beecroft from the Pawsey Supercomputing Research Centre will talk about their Nimbus Cloud systems. While Nextflow supports portability and can run on many computing infrastructures, we describe why we specifically love using Nimbus with Nextflow for many bioinformatics projects. We will describe some of the nf.co-re workflows that we have used on Nimbus and the research outcomes. We will also cover when not to use Nimbus and the alternatives we recommend.

Speakers: 

Dr Nandan Deshpande, Senior Research Bioinformatician, Sydney Informatics Hub, University of Sydney

Dr Sarah Beecroft, Bioinformatics Applications Specialist, Pawsey Supercomputing Research Centre.

When: Tuesday 20 September 2022, 1pm AEST/12:30pm ACST/11am AWST

Who the webinar is for:

This webinar is for biologists who are new to bioinformatics on the command-line and bioinformaticians and would like to use existing best practice workflows available through nf.co-re.

This webinar was recorded on 20 September 2022

The slides from this webinar will be available on Zenodo
https://zenodo.org/communities/australianbiocommons-training

See upcoming webinars and workshops on our website:
https://www.biocommons.org.au/webinars-workshops

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