🌱📦 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.

✅ 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

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 →

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.

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

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

1. Fork the repository

2. Create your component following our guidelines

3. Test thoroughly with viash test

4. Submit a pull request

• Popular bioinformatics tools missing from our collection

• Improvements to existing components

• Bug fixes and documentation enhancements

• Best practice implementations

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.

• Documentation: Viash Documentation

• Discussions: GitHub
  Discussions

• Issues: Bug Reports & Feature
  Requests

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