CI
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
125 lines
4.4 KiB
Markdown
125 lines
4.4 KiB
Markdown
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# 🌱📦 biobox
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[](https://www.viash-hub.com/packages/biobox)
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[](https://github.com/viash-hub/biobox)
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[](https://github.com/viash-hub/biobox/blob/main/LICENSE)
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[](https://github.com/viash-hub/biobox/issues)
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[](https://viash.io)
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**A curated collection of high-quality, production-ready bioinformatics
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components**
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Built with [Viash](https://viash.io), biobox provides reliable,
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containerized tools for genomics and bioinformatics workflows. Each
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component is thoroughly tested, fully documented, and designed for
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seamless integration into both standalone and Nextflow pipelines.
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## Why Choose biobox?
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✅ **Production Ready**: All components are containerized with pinned
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versions and comprehensive testing
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✅ **Nextflow Native**: Drop-in compatibility with Nextflow workflows
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✅ **Complete Documentation**: Full parameter exposure with detailed
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help and examples
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✅ **Quality Assured**: Unit tested with automated CI/CD validation
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✅ **Modern Standards**: Built with current best practices and
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maintained dependencies
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## Featured Tools
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Our collection spans the complete bioinformatics pipeline:
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**Alignment & Mapping**: BWA, Bowtie2, STAR, Kallisto, Salmon
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**Quality Control**: FastQC, Falco, MultiQC, Qualimap, NanoPlot
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**Preprocessing**: Cutadapt, fastp, Trimgalore, UMI-tools
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**Variant Calling**: BCFtools, LoFreq, SnpEff
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**File Manipulation**: SAMtools, Bedtools, seqtk
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**Assembly & Annotation**: BUSCO, AGAT, GFFread
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**Single Cell**: CellRanger, BD Rhapsody
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[View all components →](https://www.viash-hub.com/packages/biobox)
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## Quick Start
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You can run Viash components from biobox in several ways:
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**🌐 Via Viash Hub Web UI**: Interactive interface with documentation
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and examples
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**⚡ As Standalone Executables**: Direct command-line execution
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**🔄 Via Nextflow**: Local or cloud-based pipeline workflows
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For detailed instructions on each method, visit the **[Viash Hub
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documentation →](https://viash-hub.com/packages/biobox)** where each
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component page shows exactly how to run it in different environments.
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``` mermaid
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flowchart LR
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A[biobox Components] --> B[🌐 Web UI]
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A --> C[⚡ Standalone]
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A --> D[🔄 Nextflow Local]
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A --> E[☁️ Nextflow Cloud]
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style A fill:#7a4baa,color:#fff
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style B fill:#e1f5fe,color:#000
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style C fill:#e8f5e8,color:#000
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style D fill:#fff3e0,color:#000
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style E fill:#f3e5f5,color:#000
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```
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You can run components directly from Viash Hub’s launch interface. See
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[Viash Hub](https://www.viash-hub.com/packages/biobox) for more
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information.
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## Contributing
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We welcome contributions! biobox thrives on community input to expand
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our collection of high-quality bioinformatics components.
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### Quick Contribution Process
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1. **Fork** the repository
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2. **Create** your component following our guidelines
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3. **Test** thoroughly with `viash test`
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4. **Submit** a pull request
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### What We’re Looking For
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- **Popular bioinformatics tools** missing from our collection
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- **Improvements** to existing components
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- **Bug fixes** and documentation enhancements
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- **Best practice** implementations
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### Getting Started
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Check out our comprehensive guides:
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- **[Contributing
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Guidelines](https://github.com/viash-hub/biobox/blob/main/CONTRIBUTING.md)** -
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Complete development guide
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- **[Component Standards](docs/COMPONENT_DEVELOPMENT.md)** - Quality
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requirements
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- **[Testing Guide](docs/TESTING.md)** - Validation best practices
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**New to Viash?** Start with our [beginner-friendly
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issues](https://github.com/viash-hub/biobox/labels/good%20first%20issue)
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or join our [community
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discussions](https://github.com/viash-hub/biobox/discussions).
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## Community & Support
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- **Documentation**: [Viash Documentation](https://viash.io)
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- **Discussions**: [GitHub
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Discussions](https://github.com/viash-hub/biobox/discussions)
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- **Issues**: [Bug Reports & Feature
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Requests](https://github.com/viash-hub/biobox/issues)
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------------------------------------------------------------------------
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**Ready to streamline your bioinformatics workflows?** [Get started with
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biobox today →](https://www.viash-hub.com/packages/biobox)
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