Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix.

GigaScience
Justin BedőAnthony T Papenfuss

Abstract

A challenge for computational biologists is to make our analyses reproducible-i.e. 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. We 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. This lets users specify workflows in a clean, uniform way, with strong reproducibility guarantees. BioNix is implemented in the Nix expression language and is released on GitHub under the 3-clause BSD license: https://github.com/PapenfussLab/bionix (biotools:BioNix) (BioNix, RRID:SCR_017662).

References

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Key Resources (RRID) Mentioned

SCR_017662

Software Mentioned

Conda
FastQC
Python
CWL
Cuneiform
Guix Workflow Language
Docker
Bionix
Fractalide
picard

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