🌱📦 biobox

A curated collection of high-quality, production-ready bioinformatics components

Built with Viash, biobox provides reliable, containerized tools for genomics and bioinformatics workflows. Each component is thoroughly tested, fully documented, and designed for seamless integration into both standalone and Nextflow pipelines.

Why Choose biobox?

✅ Production Ready: All components are containerized with pinned versions and comprehensive testing
✅ Nextflow Native: Drop-in compatibility with Nextflow workflows
✅ Complete Documentation: Full parameter exposure with detailed help and examples
✅ Quality Assured: Unit tested with automated CI/CD validation
✅ Modern Standards: Built with current best practices and maintained dependencies

Featured Tools

Our collection spans the complete bioinformatics pipeline:

Alignment & Mapping: BWA, Bowtie2, STAR, Kallisto, Salmon
Quality Control: FastQC, Falco, MultiQC, Qualimap, NanoPlot
Preprocessing: Cutadapt, fastp, Trimgalore, UMI-tools
Variant Calling: BCFtools, LoFreq, SnpEff
File Manipulation: SAMtools, Bedtools, seqtk
Assembly & Annotation: BUSCO, AGAT, GFFread
Single Cell: CellRanger, BD Rhapsody

View all components →

Quick Start

You can run Viash components from biobox in several ways:

🌐 Via Viash Hub Web UI: Interactive interface with documentation and examples
⚡ As Standalone Executables: Direct command-line execution
🔄 Via Nextflow: Local or cloud-based pipeline workflows

For detailed instructions on each method, visit the Viash Hub documentation → where each component page shows exactly how to run it in different environments.

flowchart LR
    A[biobox Components] --> B[🌐 Web UI]
    A --> C[⚡ Standalone]
    A --> D[🔄 Nextflow Local]
    A --> E[☁️ Nextflow Cloud]
    
    style A fill:#7a4baa,color:#fff
    style B fill:#e1f5fe,color:#000
    style C fill:#e8f5e8,color:#000
    style D fill:#fff3e0,color:#000
    style E fill:#f3e5f5,color:#000

You can run components directly from Viash Hub’s launch interface. See Viash Hub for more information.

Contributing

We welcome contributions! biobox thrives on community input to expand our collection of high-quality bioinformatics components.

Quick Contribution Process

1. Fork the repository
2. Create your component following our guidelines
3. Test thoroughly with viash test
4. Submit a pull request

What We’re Looking For

• Popular bioinformatics tools missing from our collection
• Improvements to existing components
• Bug fixes and documentation enhancements
• Best practice implementations

Getting Started

Check out our comprehensive guides:

• Contributing Guidelines - Complete development guide
• Component Standards - Quality requirements
• Testing Guide - Validation best practices

New to Viash? Start with our beginner-friendly issues or join our community discussions.

Community & Support

• Documentation: Viash Documentation
• Discussions: GitHub Discussions
• Issues: Bug Reports & Feature Requests

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Ready to streamline your bioinformatics workflows? Get started with biobox today →