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Unlocking nf-core

Customising workflows for your research

This workshop will provide you with the foundational knowledge required to run and customise nf-core pipelines in a reproducible manner. The content is broken up into 2 half-day sessions. In the first session we will cover the basic principles of running nf-core pipelines. Then, in the second session we will step through various customisation scenarios using the nf-core/rnaseq pipeline. We will explore ways to adjust the pipeline parameters based on the needs of your dataset and how to configure the pipeline to run on your computational platform. See the lesson plan for details.

Trainers

  • Dr Michael Geaghan, Sydney Informatics Hub, The University of Sydney
  • Dr Cali Willet, Sydney Informatics Hub, The University of Sydney

Facilitators

  • Dr Giorgia Mori, Australian BioCommons
  • Dr Magda Antczak, Queensland Cyber Infrastructure Foundation (QCIF)
  • Dr Kristina Gagalova, Curtin University

Prerequisites

Set up requirements

Please complete the Setup Instructions before the course.

If you have any trouble, please get in contact with us ASAP.

Code of Conduct

In order to foster a positive and professional learning environment we encourage the following kinds of behaviours at all our events and on our platforms:

  • Use welcoming and inclusive language
  • Be respectful of different viewpoints and experiences
  • Gracefully accept constructive criticism
  • Focus on what is best for the community
  • Show courtesy and respect towards other community members

Our full code of conduct, with incident reporting guidelines, is available here.

Workshop schedule

Lesson Overview
Set up your computer Follow these instructions to install VS Code and login to your Nectar VM.
Session 1: Introduction to nf-core Learn fundamental ideas and skills that are essential for using Nextflow and nf-core pipelines.
Session 2: Customising nf-core Write, run, adjust, and re-run an nf-core pipeline as we step through various customisation and troubleshooting scenarios.

Course survey

Please fill out our course survey before you leave. Help us help you! 😁

Credits and acknowledgements

This workshop event and accompanying materials were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera Labs, Pawsey Supercomputing Research Centre, and Australia’s National Research Education Network (AARNet). The workshop was enabled through the Australian BioCommons - Bring Your Own Data Platforms project (Australian Research Data Commons and NCRIS via Bioplatforms Australia) and was run using data from Corley et al. 2016.

Developers

  • Dr Michael Geaghan, Sydney Informatics Hub, The University of Sydney
  • Dr Cali Willet, Sydney Informatics Hub, The University of Sydney
  • Dr Georgie Samaha, Sydney Informatics Hub, The University of Sydney
  • Dr Magda Antczak, Queensland Cyber Infrastructure Foundation (QCIF)
  • Dr Chris Hakkaart, Seqera Labs