04a5851ff8
Build pipeline: viash-hub.biobox.main-tb4cv
Source commit: 7158daa5f6
Source message: Fix bases2fastq component, update to latest practices (#190)
* wip updates
* refactor component
* assume bases2fastq follows semver
* fix version command
* add entry to changelog
* move to minor changes
4.4 KiB
🌱📦 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
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
- Fork the repository
- Create your component following our guidelines
- Test thoroughly with
viash test - 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
Ready to streamline your bioinformatics workflows? Get started with biobox today →