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
122 lines
5.0 KiB
Plaintext
122 lines
5.0 KiB
Plaintext
---
|
|
format: gfm
|
|
---
|
|
```{r setup, include=FALSE}
|
|
package <- yaml::read_yaml("_viash.yaml")
|
|
license <- paste0(package$links$repository, "/blob/main/LICENSE")
|
|
contributing <- paste0(package$links$repository, "/blob/main/CONTRIBUTING.md")
|
|
|
|
pkg <- package$name
|
|
ver <- if (!is.null(package$version)) package$version else "v0.4.0"
|
|
comp <- "bowtie2_align"
|
|
|
|
# Count components
|
|
component_dirs <- list.dirs("src", recursive = FALSE, full.names = FALSE)
|
|
component_dirs <- component_dirs[!startsWith(component_dirs, "_")]
|
|
n_tools <- length(component_dirs)
|
|
```
|
|
|
|
# 🌱📦 `r pkg`
|
|
|
|
[](https://www.viash-hub.com/packages/`r pkg`)
|
|
[](`r package$links$repository`)
|
|
[](`r license`)
|
|
[](`r package$links$issue_tracker`)
|
|
[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", package$viash_version)`-blue.svg)](https://viash.io)
|
|
|
|
**A curated collection of high-quality, production-ready bioinformatics components**
|
|
|
|
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.
|
|
|
|
## Why Choose `r pkg`?
|
|
|
|
✅ **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 →](https://www.viash-hub.com/packages/`r pkg`)
|
|
|
|
## Quick Start
|
|
|
|
You can run Viash components from `r pkg` 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 →](https://viash-hub.com/packages/`r pkg`)** where each component page shows exactly how to run it in different environments.
|
|
|
|
```{r mmd, echo=FALSE, results='asis'}
|
|
cat(
|
|
"```mermaid\n",
|
|
"flowchart LR\n",
|
|
" A[", pkg, " Components] --> B[🌐 Web UI]\n",
|
|
" A --> C[⚡ Standalone]\n",
|
|
" A --> D[🔄 Nextflow Local]\n",
|
|
" A --> E[☁️ Nextflow Cloud]\n",
|
|
" \n",
|
|
" style A fill:#7a4baa,color:#fff\n",
|
|
" style B fill:#e1f5fe,color:#000\n",
|
|
" style C fill:#e8f5e8,color:#000\n",
|
|
" style D fill:#fff3e0,color:#000\n",
|
|
" style E fill:#f3e5f5,color:#000\n",
|
|
"```\n",
|
|
sep = ""
|
|
)
|
|
```
|
|
|
|
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.
|
|
|
|
|
|
## Contributing
|
|
|
|
We welcome contributions! `r pkg` 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](`r contributing`)** - Complete development guide
|
|
- **[Component Standards](docs/COMPONENT_DEVELOPMENT.md)** - Quality requirements
|
|
- **[Testing Guide](docs/TESTING.md)** - Validation best practices
|
|
|
|
**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).
|
|
|
|
## Community & Support
|
|
|
|
- **Documentation**: [Viash Documentation](https://viash.io)
|
|
- **Discussions**: [GitHub Discussions](https://github.com/viash-hub/biobox/discussions)
|
|
- **Issues**: [Bug Reports & Feature Requests](https://github.com/viash-hub/biobox/issues)
|
|
|
|
---
|
|
|
|
**Ready to streamline your bioinformatics workflows?** [Get started with `r pkg` today →](https://www.viash-hub.com/packages/`r pkg`)
|