These components can be used to:
- Seamlessly execute your script natively on the host platform.
- Easily resolve any dependencies by running the script in an automatically generated Docker container.
- Automatically wrap your script in an executable with a CLI and
- Combine multiple scripts in a Nextflow pipeline.
- Unit-test your script to ensure that it works at all times.
Example use cases
Here are a few use cases which serve as motivation for Viash:
The script you wrote needs to be made more user friendly by using a CLI that describes the accepted arguments.By wrapping your script in a component, Viash provides an intuitive CLI out of the box.
You want to combine several tools in a pipeline and every tool has specific requirements on how they should be run. Even worse: some requirements might directly conflict with each other.Viash can help you by running each tool in its own Docker container with specific software versions. You can turn the components into a pipeline by using scripting or Nextflow.
Your next data analysis project is very similar to the previous project, so you copy and paste the source code. Unfortunately, you detect a bug in some of your code, so now you need to go back and fix the same bug in all the different projects.By using Viash, you can split the project up in reusable components, and you’ll only need to apply fixes in a single location.
You want to look back at a data analysis you performed two years ago. Unfortunately, the software you used back then is not supported anymore, or the newest version produces totally different results.With Viash you can package the older version together with its dependencies in an executable so you don’t have to worry about conflicts or deprecated versions.
You developed a Jupyter notebook report for a data analysis. You wish to share it with your colleague, only to spend two hours installing your Conda stack on their laptop.Viash can help you by bundling your scripts along with the dependencies into components that can run in a Docker container.
The menu on the left contains all guides per category on using Viash. Most topics are in order of complexity per category.
To start off, we recommend you take a look at the following guides:
Once you have Viash installed and have taken a look at the basics, check out one of the language specific guides in the CREATING VIASH COMPONENTS category to learn how to create your very own component in your preferred language.
The following pages are good starting points to delve a bit deeper into using Viash:
Once you’re comfortable with the basics, here are some more advanced topics:
- Creating a Scripted Pipeline
- Nextflow Platform
- Creating a Nextflow Pipeline
- Dynamic Config Modding
If you wish to contribute to Viash or the documentation, take a look at our Contributing Guidelines.