biobox/README.md

🌱📦 biobox

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

Introduction

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.

Example Usage

Viash components in biobox can be run in various ways:

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.

2. Via the Viash CLI

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

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.

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 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.

4. As a dependency

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

dependencies:
  - name: arriba
    repository: vsh://biobox@v0.3.1

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

Contributing

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.