🛠📦 toolbox

A collection of curated command-line tools for general IT tasks, built with Viash.

Introduction

toolbox provides a versatile suite of IT components, following the robust Viash (https://viash.io) framework. This package focuses on delivering reliable, standalone tools that can be easily integrated into larger computational workflows.

The core philosophy emphasizes reusability, reproducibility, and adherence to best practices in component creation. Key features of toolbox components include:

• Standalone & Nextflow Ready: Execute components directly from the command line or seamlessly incorporate them into Nextflow workflows.
• High Quality Standards:
  • Comprehensive documentation for each component and its parameters.
  • Full exposure of the underlying tool’s arguments for maximum flexibility.
  • Containerized (Docker) to ensure consistent environments and manage dependencies, leading to enhanced reproducibility.
  • Unit tested to verify functionality and ensure reliability.

Example Usage

Viash components in toolbox can be run in various ways:

flowchart TD
    A[toolbox v0.1.0] --> 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://toolbox@v0.1.0/yq -- --help

viash run vsh://toolbox@v0.1.0/yq -- \
  --input path/to/input.yaml \
  --output output.yaml

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/toolbox \
  -revision v0.1.0 \
  -main-script target/nextflow/yq/main.nf \
  -latest -resume \
  -profile docker \
  --input path/to/input.yaml \
  --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: yq
    repository: vsh://toolbox@v0.1.0

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.