NF-Core: Community-based best practice pipeline development in Nextflow

 

Alexander Peltzer

Quantitative Biology Center (QBiC) Tübingen

http://bit.ly/ismb2018-nfcore

@alex_peltzer

Outlook

 

• Challenges in computational biology
• Basic introduction to Nextflow
• Introduction to NF-core project

Challenges: Big Data

 

• Data in computational biology is
  • big (PB scale)
  • diverse (sequencing, proteomics, metabolomics ...)
  • erroneous (e.g. contains sequencing errors)

 

 

We need methods and tools to analyze such data!

Challenges: Software dependencies

 

 

Workflows / Pipelines consist of

 

• various different tools
• typically dozens of individual methods

 

Complex dependency management!

 

Challenges: Reproducibility

 

• Large-scale projects more common today
  • 1,000 Genomes Project
  • 100,000 Genomes Project UK
• Reproduce results with older data / integrate with newer data

 

 

 Many paper results are not reproducible!

 

Nextflow

 

• Custom DSL (domain-specific language) for
  • fast prototyping
  • enabling task composition
  • easy parallelization
• Self-contained: Containerize tasks (e.g. with Docker)
• Isolation of dependencies: Keep container - rerun analysis at any point!

• Community effort to collect production ready analysis pipelines
• Save time in development, more testing, more updates

 

https://nf-co.re

 

Phil Ewels

Alex Peltzer

Sven Fillinger

Andreas Wilm

Maxime Garcia

+ many others!

Tiffany Delhomme

All pipelines adhere to requirements

• Nextflow based
• MIT license
• Software bundled in Docker / Singularity
• Continuous integration testing (e.g. Travis CI)
• Stable release tags
• Common pipeline usage and structure

Optional requirements

 

• Software bundled in Bioconda
• Optimized output formats (e.g. CRAM)
• Explicit support for cloud environments (AWS)
• Benchmarks for running on such environments

Need help?

 

• Cookiecutter: To get a skeleton for new pipelines
• Linting app: To check what conforms with nf-co.re
• Gitter: To communicate with the community!

 

Comes with interactive reports!

Comes with proper documentation!

... and a lot more!

Acknowledgements

Phil Ewels (SciLifeLab, Stockholm)

Maxime Garcia (SciLifeLab, Stockholm)

Sven Fillinger (QBiC, Tübingen)

Paolo di Tommaso (CRG, Barcelona)

Evan Floden (CRG, Barcelona)

Andreas Wilm (A* Singapore, Singapore)

Tiffany Delhomme (IARC, Paris)