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143 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, standalone bioinformatics
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components built with [Viash](https://viash.io).
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## Introduction
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`biobox` offers a suite of reliable bioinformatics components, similar
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to [nf-core/modules](https://github.com/nf-core/modules) and
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[snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),
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but built using the [Viash](https://viash.io) framework.
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This approach emphasizes **reusability**, **reproducibility**, and
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adherence to **best practices**. Key features of `biobox` components
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include:
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- **Standalone & Nextflow Ready:** Run components directly via the
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command line or seamlessly integrate them into Nextflow workflows.
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- **High Quality Standards:**
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- Comprehensive documentation for components and parameters.
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- Full exposure of underlying tool arguments.
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- Containerized (Docker) for dependency management and
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reproducibility.
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- Unit tested for verified functionality.
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## Example Usage
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Viash components in biobox can be run in various ways:
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``` mermaid lang="mermaid"
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flowchart TD
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A[biobox v0.3.0] --> B(Viash Hub Launch)
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A --> C(Viash CLI)
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A --> D(Nextflow CLI)
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A --> E(Seqera Cloud)
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A --> F(As a dependency)
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```
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### 1. Via the Viash Hub Launch interface
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You can run this component directly from the Viash Hub [Launch
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interface](https://www.viash-hub.com/launch?package=biobox&version=v0.3.0&component=arriba&runner=Executable).
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### 2. Via the Viash CLI
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You can run this component directly from the command line using the
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Viash CLI.
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``` bash
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viash run vsh://biobox@v0.3.0/arriba -- --help
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viash run vsh://biobox@v0.3.0/arriba -- \
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--bam path/to/input.bam \
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--genome path/to/genome.fa \
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--gene_annotation path/to/annotation.gtf \
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--fusions path/to/output.txt
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```
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This will run the component with the specified input files and output
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the results to the specified output file.
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### 3. Via the Nextflow CLI or Seqera Cloud
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You can run this component as a Nextflow pipeline.
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``` bash
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nextflow run https://packages.viash-hub.com/vsh/biobox \
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-revision v0.3.0 \
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-main-script target/nextflow/arriba/main.nf \
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-latest -resume \
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-profile docker \
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--bam path/to/input.bam \
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--genome path/to/genome.fa \
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--gene_annotation path/to/annotation.gtf \
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--publish_dir path/to/output
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```
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**Note:** Make sure that the [Nextflow
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SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration) is
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set up properly. You can do this by adding the following lines to your
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`~/.nextflow/scm` file:
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``` groovy
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providers.vsh.platform = 'gitlab'
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providers.vsh.server = 'https://packages.viash-hub.com'
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```
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**Tip:** This will also work with Seqera Cloud or other
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Nextflow-compatible platforms.
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### 4. As a dependency
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In your Viash config file (`config.vsh.yaml`), you can add this
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component as a dependency:
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``` yaml
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dependencies:
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- name: arriba
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repository: vsh://biobox@v0.3.0
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```
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**Tip:** See the [Viash
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documentation](https://viash.io/guide/nextflow_vdsl3/create-a-pipeline.html#pipeline-as-a-component)
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for more details on how to use Viash components as a dependency in your
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own Nextflow workflows.
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## Contributing
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Contributions are welcome! We aim to build a comprehensive collection of
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high-quality bioinformatics components. If you’d like to contribute,
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please follow these general steps:
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1. Find a component to contribute
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2. Add config template
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3. Fill in the metadata
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4. Find a suitable container
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5. Create help file
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6. Create or fetch test data
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7. Add arguments for the input files
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8. Add arguments for the output files
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9. Add arguments for the other arguments
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10. Add a Docker engine
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11. Write a runner script
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12. Create test script
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13. Create a `/var/software_versions.txt` file
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See the
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[CONTRIBUTING](https://github.com/viash-hub/biobox/blob/main/CONTRIBUTING.md)
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file for more details.
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