Components

OpenProblems uses Viash components to facilitate the separation of component functionality from the pipeline workflow.

A Viash component is a combination of a code block or script and a small amount of metadata that makes it easy to generate pipeline modules, facilitating the separation of component functionality from the pipeline workflow (Cannoodt et al. 2021). This enables developers to create reusable, modular, and robust components for OpenProblems, focusing on the specific functionality without having to worry about the chosen pipeline framework.

Cannoodt, Robrecht, Hendrik Cannoodt, Eric Van de Kerckhove, Andy Boschmans, Dries De Maeyer, and Toni Verbeiren. 2021. “Viash: From Scripts to Pipelines.” arXiv. https://doi.org/10.48550/ARXIV.2110.11494.

A Viash component consists of three main parts: a Viash config, a script, and one or more unit tests (Figure 1).

Figure 1: Viash supports robust pipeline development by allowing users to build their component as a standalone executable (with auto-generated CLI), build a Docker container to run the script inside, or turn the component into a standalone Nextflow module.

Example component

When creating a new Viash component, you will need to create a script and a config file. Below is an example of a simple Viash component written in Python. For a detailed explanation of the structure of a Viash component in more programming languages (e.g. Bash, Python, R), please visit review documentation on how to create a Viash component.

Script

To help with prototyping, a Viash component’s script should be runnable. You can do this by defining a Viash placeholder code block denoted by the ## VIASH START and ## VIASH END comments.

The Viash placeholder should contain a dictionary (or named list) which contains example values for all of the input/output arguments your component needs. During execution, Viash will remove the placeholder and replace it with the actual parameter values at runtime.

script.py

import anndata

## VIASH START
# Note: This codeblock is for prototyping and
# is removed by Viash at runtime.
par = {
  'input': 'test_resource.txt',
  'output': 'output.txt'
}
## VIASH END

# Print par
print(f"par: {par}")

# Read input file
adata = anndata.read_h5ad(par["input"])

# Print adata
print(f"adata: {adata}")

# Write output file
adata.write_h5ad(par["output"])

Tip

It’s possible to store helper functions in separate files. Visit the Viash documentation for more information.

Viash config

Next, we’ll write a Viash config file for this component.

config.vsh.yaml

functionality:
  name: mycomponent
  description: |
    A multiline description.
  arguments:
    - name: "--input"
      type: file
      description: Input h5ad
      example: input.h5ad
      required: true
    - name: "--output"
      type: file
      direction: output
      description: Output g5ad
      example: output.h5ad
      required: true
  resources:
    - type: python_script
      path: script.py
    tests:
    - type: python_script
      path: test.py
platforms:
  - type: docker
      image: "python:3.10"
      setup:
        - type: python
          pypi: anndata
  - type: native
  - type: nextflow

Tip

After adding more arguments to the config, you can update your script using the viash config inject

Component format specifications

OpenProblems tasks contain specifications for the common config fields between the same component types. These specifications are defined in the src/tasks/*/comp_*.yaml files. For more information on how these specifications are formatted, see “Design the API”.