🪡📦 craftbox

A collection of custom-tailored scripts and applied utilities built with
Viash.

craftbox is a curated collection of custom scripts and utilities
designed to tackle context-specific tasks.

Emphasizing the Viash principles, craftbox components aim for
reusability, reproducibility, and adherence to best
practices. Key features generally include:

• Standalone & Nextflow Ready: Components are built to run directly
  via the command line or be smoothly integrated into Nextflow
  workflows.

• Custom Implementations: Contains scripts and tools developed for
  particular tasks that may not be found in broader collections.

• High Quality Standards (promoted by Viash):

  • Clear documentation for components and their parameters.

  • Full exposure of underlying script/tool arguments for fine-grained
    control.

  • Containerized (Docker) to ensure dependency management and a
    consistent, reproducible runtime environment.

  • Unit tested where applicable to ensure components function as
    expected.

Viash components in craftbox 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://craftbox@v0.3.3/concat_rtext -- --help

viash run vsh://craftbox@v0.3.3/concat_rtext -- \  
  --input path/to/input.txt \  
  --input path/to/compressed.txt.gz \  
  --output 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/craftbox \  
  -revision v0.3.3 \  
  -main-script target/nextflow/concat_rtext/main.nf \  
  -latest -resume \  
  -profile docker \  
  --input "path/to/input.txt;path/to/compressed.txt.gz" \  
  --output path/to/output.txt  

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: concat_rtext  
    repository: vsh://craftbox@v0.3.3  

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.