🌱📦 biobox

A curated collection of high-quality, standalone bioinformatics
components built with Viash.

biobox offers a suite of reliable bioinformatics components, similar
to nf-core/modules and
snakemake-wrappers/bio,
but built using the Viash 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.

Viash components in biobox can be run in various ways:

You can run this component directly from the Viash Hub Launch
interface.

You can run this component directly from the command line using the
Viash CLI.

viash run vsh://biobox@v0.3.0/arriba -- --help

viash run vsh://biobox@v0.3.0/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.

You can run this component as a Nextflow pipeline.

nextflow run https://packages.viash-hub.com/vsh/biobox \  
  -revision v0.3.0 \  
  -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 is
set up properly. You can do this by adding the following lines to your
~/.nextflow/scm file:

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.

In your Viash config file (config.vsh.yaml), you can add this
component as a dependency:

dependencies:  
  - name: arriba  
    repository: vsh://biobox@v0.3.0  

Tip: See the Viash
documentation
for more details on how to use Viash components as a dependency in your
own Nextflow workflows.

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

3. Fill in the metadata

4. Find a suitable container

5. Create help file

6. Create or fetch test data

7. Add arguments for the input files

8. Add arguments for the output files

9. Add arguments for the other arguments

10. Add a Docker engine

11. Write a runner script

12. Create test script

13. Create a /var/software_versions.txt file

See the
CONTRIBUTING
file for more details.