Guide
Viash Component
A Viash component is a modular software component used in building data pipelines. It consists of a script written in one of the supported scripting languages (Bash, Python, R, Scala, JS, or C#) and a metadata file that outlines its dependencies. Viash components can be converted into standalone executables.
- Create a new component: Building a reproducible Viash component.
- Add dependencies: Adding custom dependencies to a component.
- Add resources: Accessing additional resources inside a Viash component.
- Use helper functions: How to load helper functions.
- Par and meta variables: A showcase of the available variables and meta-variables.
- Unit testing: How to ensure high quality components.
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Viash Project
A Viash project is a collection of Viash components, typically designed to work together to perform a specific task. Viash projects enable batch processing, making it easier to handle multiple components and data sets simultaneously.
- Structure: The project already contains three components which are used to create a Nextflow pipeline with the following topology:
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Batch processing: Within this project it’s possible to do all of the same things mentioned in the “Component” guide such as build a target executable with
viash buildand test a component with… -
Package config: A
_viash.yamlfile in the root of the package repository is called a Viash package config. It allows defining project-wide settings such as the location of the Viash… - IDE setup: Since a Viash components consists of a script in one of the supported languages and a YAML file, you can use any editor of your choosing to create these files.
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Viash+Nextflow VDSL3
VDSL3 is a Nextflow module generated by Viash from a script, allowing users to design and run scalable, reproducible data pipelines without requiring expertise in Nextflow.
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Create and use a module: Creating a VDSL3 module is as simple as adding
{ type: nextflow }to therunnerssection in the Viash config. Luckily, our previous example already contained such an entry: - Create a pipeline: This guide explains how to create an example pipeline that’s closer to a typical use-case of a Nextflow bioinformatics pipeline.
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