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Build pipeline: viash-hub.biobox.main-nmzjs Source commit: b0db228825 Source message: Update readme (#177) * update image * add changelog * make readme more generic * fix url * make images relative again
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 # 🌱📦 biobox

-[![ViashHub](https://img.shields.io/badge/ViashHub-biobox-7a4baa.png)](https://web.viash-hub.com/packages/biobox)
-[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fbiobox-blue.png)](https://github.com/viash-hub/biobox)
+[![ViashHub](https://img.shields.io/badge/ViashHub-biobox-7a4baa.svg)](https://www.viash-hub.com/packages/biobox)
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fbiobox-blue.svg)](https://github.com/viash-hub/biobox)
 [![GitHub
-License](https://img.shields.io/github/license/viash-hub/biobox.png)](https://github.com/viash-hub/biobox/blob/main/LICENSE)
+License](https://img.shields.io/github/license/viash-hub/biobox.svg)](https://github.com/viash-hub/biobox/blob/main/LICENSE)
 [![GitHub
-Issues](https://img.shields.io/github/issues/viash-hub/biobox.png)](https://github.com/viash-hub/biobox/issues)
+Issues](https://img.shields.io/github/issues/viash-hub/biobox.svg)](https://github.com/viash-hub/biobox/issues)
 [![Viash
-version](https://img.shields.io/badge/Viash-v0.9.0--RC6-blue)](https://viash.io)
+version](https://img.shields.io/badge/Viash-v0.9.4-blue.svg)](https://viash.io)

-A collection of bioinformatics tools for working with sequence data.
+A curated collection of high-quality, standalone bioinformatics
+components built with [Viash](https://viash.io).

-## Objectives
+## Introduction

- **Reusability**: Facilitating the use of components across various
-  projects and contexts.
- **Reproducibility**: Ensuring that components are reproducible and can
-  be easily shared.
- **Best Practices**: Adhering to established standards in software
-  development and bioinformatics.
+`biobox` offers a suite of reliable bioinformatics components, similar
+to [nf-core/modules](https://github.com/nf-core/modules) and
+[snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),
+but built using the [Viash](https://viash.io) framework.
+
+This approach emphasizes **reusability**, **reproducibility**, and
+adherence to **best practices**. Key features of `biobox` components
+include:
+
+- **Standalone & Nextflow Ready:** Run components directly via the
+  command line or seamlessly integrate them into Nextflow workflows.
+- **High Quality Standards:**
+  - Comprehensive documentation for components and parameters.
+  - Full exposure of underlying tool arguments.
+  - Containerized (Docker) for dependency management and
+    reproducibility.
+  - Unit tested for verified functionality.
+
+## Example Usage
+
+Viash components in biobox can be run in various ways:
+
+``` mermaid lang="mermaid"
+flowchart TD
+    A[biobox v0.3.1] --> B(Viash Hub Launch)
+    A --> C(Viash CLI)
+    A --> D(Nextflow CLI)
+    A --> E(Seqera Cloud)
+    A --> F(As a dependency)
+```
+
+### 1. Via the Viash Hub Launch interface
+
+You can run this component directly from the Viash Hub [Launch
+interface](https://www.viash-hub.com/launch?package=biobox&version=v0.3.1&component=arriba&runner=Executable).
+
+![](docs/viash-hub.png)
+
+### 2. Via the Viash CLI
+
+You can run this component directly from the command line using the
+Viash CLI.
+
+``` bash
+viash run vsh://biobox@v0.3.1/arriba -- --help
+
+viash run vsh://biobox@v0.3.1/arriba -- \
+  --bam path/to/input.bam \
+  --genome path/to/genome.fa \
+  --gene_annotation path/to/annotation.gtf \
+  --fusions path/to/output.txt
+```
+
+This will run the component with the specified input files and output
+the results to the specified output file.
+
+### 3. Via the Nextflow CLI or Seqera Cloud
+
+You can run this component as a Nextflow pipeline.
+
+``` bash
+nextflow run https://packages.viash-hub.com/vsh/biobox \
+  -revision v0.3.1 \
+  -main-script target/nextflow/arriba/main.nf \
+  -latest -resume \
+  -profile docker \
+  --bam path/to/input.bam \
+  --genome path/to/genome.fa \
+  --gene_annotation path/to/annotation.gtf \
+  --publish_dir path/to/output
+```
+
+**Note:** Make sure that the [Nextflow
+SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration) is
+set up properly. You can do this by adding the following lines to your
+`~/.nextflow/scm` file:
+
+``` groovy
+providers.vsh.platform = 'gitlab'
+providers.vsh.server = 'https://packages.viash-hub.com'
+```
+
+**Tip:** This will also work with Seqera Cloud or other
+Nextflow-compatible platforms.
+
+### 4. As a dependency
+
+In your Viash config file (`config.vsh.yaml`), you can add this
+component as a dependency:
+
+``` yaml
+dependencies:
+  - name: arriba
+    repository: vsh://biobox@v0.3.1
+```
+
+**Tip:** See the [Viash
+documentation](https://viash.io/guide/nextflow_vdsl3/create-a-pipeline.html#pipeline-as-a-component)
+for more details on how to use Viash components as a dependency in your
+own Nextflow workflows.

 ## Contributing

-We encourage contributions from the community. To contribute:
-
-1.  **Fork the Repository**: Start by forking this repository to your
-    account.
-2.  **Develop Your Component**: Create your Viash component, ensuring it
-    aligns with our best practices (detailed below).
-3.  **Submit a Pull Request**: After testing your component, submit a
-    pull request for review.
-
-## Contribution Guidelines
-
-The contribution guidelines describes which steps you should follow to
-contribute a component to this repository.
+Contributions are welcome! We aim to build a comprehensive collection of
+high-quality bioinformatics components. If you’d like to contribute,
+please follow these general steps:

 1.  Find a component to contribute
 2.  Add config template
@@ -55,18 +140,3 @@ contribute a component to this repository.
 See the
 [CONTRIBUTING](https://github.com/viash-hub/biobox/blob/main/CONTRIBUTING.md)
 file for more details.
-
-## Support and Community
-
-For support, questions, or to join our community:
-
- **Issues**: Submit questions or issues via the [GitHub issue
-  tracker](https://github.com/viash-hub/biobox/issues).
- **Discussions**: Join our discussions via [GitHub
-  Discussions](https://github.com/viash-hub/biobox/discussions).
-
-## License
-
-This repository is licensed under an MIT license. See the
-[LICENSE](https://github.com/viash-hub/biobox/blob/main/LICENSE) file
-for details.