Bioinformatics Seminars

Current Bioinformatics Seminar

8 December 2020

BioNix: functional, reproducible bioinformatics workflows

Justin Bedo
WEHI Bioinformatics

A challenge for computational biologists is to make our analyses reproducible - that is, easy to rerun, combine, and share, with the assurance that equivalent runs will generate identical results. Current best practice aims at this using a combination of package managers, workflow engines, and containers. In this talk I will present BioNix, a lightweight library built on the Nix deployment system. BioNix manages software dependencies, computational environments, and workflow stages together using a single abstraction: pure functions. BioNix lets users specify workflows in a clean, uniform way, with strong reproducibility guarantees. I will also discuss the application of BioNix to the Stafford Fox Rare Cancer project. Within this project BioNix has been used to manage a complicated workflow across >100 whole genome and whole exome sequences. I will discuss lessons learnt from this application and the future direction of BioNix.


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