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Reproducible Bioinformatics Workflows with Nextflow and nf-core


Nextflow is workflow management software that enables the writing of scalable and reproducible scientific workflows. It can integrate various software packages and environment management systems from environment modules to Docker, Singularity, and Conda. It allows for existing pipelines written in common scripting languages, such as R and Python, to be seamlessly coupled together. It implements a Domain Specific Language (DSL) that simplifies the implementation and running of workflows on cloud or high-performance computing (HPC) infrastructures.

This lesson also introduces nf-core, a community-driven platform, which provides peer-reviewed best practice analysis pipelines written in Nextflow.


Session 1

  • Introduction to Session 1
  • Introduction to Nextflow
  • Introduction to nf-core
  • Configuring nf-core pipelines
  • nf-core tools for users

Session 2

  • Introduction to Session 2
  • nf-core/sarek
  • Configuring your run
  • Configuring your deployment


This workshop material was developed by Chris Hakkaart (Seqera Labs) with a huge amount of support from George Wiggins (University of Otago; Genetics Otago), Ben Halliday (University of Otago; Genetics Otago), and Dinindu Senanayake (NeSI; Genomics Aotearoa).

The workshop content was inspired by material written for Foundational Nextflow Training and the Reproducible workflows with nf-core run by Sydney Informatics Hub, University of Sydney.