CI
576c71bb0f
Build pipeline: viash-hub.biobox.v0.4.x-58lg9
Source commit: 736f18e988
Source message: Merge remote-tracking branch 'origin/main' into v0.4.x
122 lines
5.0 KiB
Plaintext
122 lines
5.0 KiB
Plaintext
---
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format: gfm
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---
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```{r setup, include=FALSE}
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package <- yaml::read_yaml("_viash.yaml")
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license <- paste0(package$links$repository, "/blob/main/LICENSE")
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contributing <- paste0(package$links$repository, "/blob/main/CONTRIBUTING.md")
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pkg <- package$name
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ver <- if (!is.null(package$version)) package$version else "v0.4.0"
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comp <- "bowtie2_align"
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# Count components
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component_dirs <- list.dirs("src", recursive = FALSE, full.names = FALSE)
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component_dirs <- component_dirs[!startsWith(component_dirs, "_")]
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n_tools <- length(component_dirs)
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```
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# 🌱📦 `r pkg`
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[](https://www.viash-hub.com/packages/`r pkg`)
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[](`r package$links$repository`)
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[](`r license`)
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[](`r package$links$issue_tracker`)
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[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", package$viash_version)`-blue.svg)](https://viash.io)
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**A curated collection of high-quality, production-ready bioinformatics components**
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Built with [Viash](https://viash.io), `r pkg` 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.
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## Why Choose `r pkg`?
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✅ **Production Ready**: All components are containerized with pinned 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 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 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/`r pkg`)
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## Quick Start
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You can run Viash components from `r pkg` in several ways:
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**🌐 Via Viash Hub Web UI**: Interactive interface with documentation 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 documentation →](https://viash-hub.com/packages/`r pkg`)** where each component page shows exactly how to run it in different environments.
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```{r mmd, echo=FALSE, results='asis'}
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cat(
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"```mermaid\n",
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"flowchart LR\n",
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" A[", pkg, " Components] --> B[🌐 Web UI]\n",
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" A --> C[⚡ Standalone]\n",
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" A --> D[🔄 Nextflow Local]\n",
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" A --> E[☁️ Nextflow Cloud]\n",
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" \n",
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" style A fill:#7a4baa,color:#fff\n",
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" style B fill:#e1f5fe,color:#000\n",
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" style C fill:#e8f5e8,color:#000\n",
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" style D fill:#fff3e0,color:#000\n",
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" style E fill:#f3e5f5,color:#000\n",
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"```\n",
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sep = ""
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)
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```
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You can run components directly from Viash Hub's launch interface. See [Viash Hub](https://www.viash-hub.com/packages/`r pkg`) for more information.
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## Contributing
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We welcome contributions! `r pkg` thrives on community input to expand 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 Guidelines](`r contributing`)** - Complete development guide
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- **[Component Standards](docs/COMPONENT_DEVELOPMENT.md)** - Quality 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 issues](https://github.com/viash-hub/biobox/labels/good%20first%20issue) or join our [community 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 Discussions](https://github.com/viash-hub/biobox/discussions)
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- **Issues**: [Bug Reports & Feature 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 `r pkg` today →](https://www.viash-hub.com/packages/`r pkg`)
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