README.qmd

---
title: "OpenProblems v2"
format: gfm
toc: false
engine: knitr
---

Formalizing and benchmarking open problems in single-cell genomics.

[**Visit the Open Problems Website.**](https://openproblems.bio/)

To get started with developing a new method or metric, please see the [OpenProblems documentation](https://openproblems.bio/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](https://github.com/openproblems-bio/openproblems-v2/releases) is fully reproducible, since all containers are published on the [GitHub Container Registry](https://github.com/orgs/openproblems-bio/packages?repo_name=openproblems-v2).