Viash.io
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Viash: A Meta-Framework for Building Reusable Workflow Modules (2024)
publication
viash
workflows
Cannoodt, R., Cannoodt, H., Schaumont, D., Waldrant, K., Van de Kerckhove, E., Boschmans, A., De Maeyer, D., & Verbeiren, T. (2024).
Viash
Encapsulate all knowledge, tools, scripts, and operations into a single, easily usable and integrable modular building block for pipeline integration solving all dependencies.
Keywords
dependency hell, RNA-seq analyses, Nextflow Integration, Next Generations Sequencing NGS, Docker Containerization for R&D, Bioinformatics, Biotech, Workflows, DataAnalysis, Pipelines, Automation, Infrastructure, Deployment, Optimization, Scalability
An Open Source Tool to Simplify Biotech Data Analysis Development
Viash
Viash is an open-source tool that simplifies and standardises data analysis development in
biotech.
By automating boilerplate code generation and producing ready-to-run modules,
Viash allows researchers to focus on innovation rather than tedious operational maintenance.
This leads to streamlined efficiency and flexibility.
Open Source
As an open-source tool, Viash enhances academia-industry collaboration by converting academic scripts into industry-ready solutions.
Ready-to-Run
Viash creates ready-to-run modules, standardizing biotech data analysis across CLI, cloud, and HPC. It ensures reproducibility, scalability and consistency.
Focus on Innovation
Viash separates science from operations, allowing researchers to focus on core research while Viash manages operational tasks, reducing the need for operational tech expertise.
Streamlined Efficiency
Viash optimizes resource management, resulting in a cost reduction and separation of duties to ensure productivity and adaptability.
We tackle key challenges in custom data analysis development
Automate Boilerplate Code for Streamlined Efficiency
Simplify your development process by automating the development of
repetitive boilerplate code, allowing you to focus on innovation and delivering high-quality
solutions faster.
Viash simplifies and standardises data analysis, making it more efficient and adaptable.
DEVELOP
Source Your Core: Writing the Foundation Script
Start by writing or finding a script in any common scripting language for the core task. This script forms the foundation for a modular, reusable Viash component.
Configure Your Needs
Create a configuration file to define your script’s parameters and dependencies. This file controls operational behavior without altering the source code. Combined with your script and optional unit tests, it forms the Viash Component.
BUILD
Generate ready-to-use modules
With a single CLI command, the Viash module is built from the Viash component, creating a ready-to-use module tailored to your needs. The Viash module ensures seamless integration and consistent execution across environments.
Viash Module Executables
By building the module, Viash has turned your source script into a runtime container as well as a Nextflow executable. Viash ensures reproducibility, scalability, easy execution and simpliefied troubleshooting.
DEPLOY
Ready-to-Run
Running a Viash module executables is straightforward. With a single CLI command, the runtime container or Nextflow module can be executed. Viash ensures consistent performance across environments.
Iterate
Easily update your core code and configurations, then rebuild the module with a single CLI command. Quickly adapt to changes and enhance your data workflows with each iteration.
Viash: Core Concepts
Polyglot
Viash supprts multiple scripting languages and is cross-platform compatible, enabling seamless integration across various technologies.
Modular
Viash turns your source scripts into self-contained executables. They can easily be run as stand-alone modules, combined with other modules to build workflows, or integrated into existing workflows.
Flexibility
Viash supports a wide range of tools and platforms, making it adaptable to various research needs
and
computational environments.
Viash Component
The Viash component is a foundational unit that includes your source script, an optional unit test script and a configuration file. It encapsulates your scientific expertise and serves as a key step in your data processing workflow.
Build
The Viash build process automatically transforms your component into a ready-to-run executable module.
Viash Module
The Viash module is a self-contained executable that can be integrated and reused easily in
your workflows, ensuring consistency and scalability. The Viash module overcomes operational
challenges, reduces errors, and streamlines deployment.
We can assist you
in refining your data analysis development
with expert support and training
Explore Viash’s Technical Details_
Viash Insights
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