OpenProblems v2

Formalizing and benchmarking open problems in single-cell genomics.

Visit the Open Problems Website.

To get started with developing a new method or metric, please see the OpenProblems documentation.

Benefits of using Viash

The pipeline is language-agnostic

This means that each component can be written in whatever scripting language the user desires. By default, Viash supports wrapping the following scripting languages: Bash, Python, R, JavaScript, and Scala. If Viash doesn’t support your preferred scripting language, you can still write a Bash script which calls your desired programming language.

One Docker container per component

Viash builds one Docker container per component. While this results in some initial computational overhead, this makes it a lot easier to add a new component to the pipeline with dependencies which might conflict with those of other components.

Reproducible components

A component built by viash is meant to be reproducible. All executables and Nextflow modules in the target/ folder in one of the releases is fully reproducible, since all containers are published on the GitHub Container Registry.