Add a method

A method is a technique to solve a specific problem when analyzing omics data. Its performance is assessed by comparing it to other methods and control methods.

This guide will show you how to create a new Viash component. In the following we will show examples for both Python and R. Note that the Task template repo is used throughout the guide, so make sure to replace any occurrences of "task_template" with your task of interest.

Step 1: Create a new component

Use the create_*_method.sh script found in the scripts repository to start creating a new method. Open the script and update the name parameter to the desired name of the method.

Change the --name to a unique name for your method. It must match the regex [a-z][a-z0-9_]* (snakecase).

• A config file contains metadata of the component and the dependencies required to run it. In steps 2 and 3 we will fill in the required information.
• A script contains the code to run the method. In step 4 we will edit the script.

Step 2: Fill in metadata

The Viash config contains metadata of your method, which script is used to run it, and the required dependencies.

Generated config file

This is what the config.vsh.yaml generated by the create_component component looks like:

Required metadata fields

Please edit info section in the config file to fill in the necessary metadata.

• .merge: The API specifies which type of component this is. It contains specifications for:

  • The input/output files
  • Common parameters
  • A unit test

• .name: A unique identifier. Can only contain lowercase letters, numbers or underscores.

• .label: A unique, human-readable, short label. Used for creating summary tables and visualizations.

• .summary: A one sentence summary of purpose and methodology. Used for creating an overview tables.

• .description: A longer description (one or more paragraphs). Used for creating reference documentation and supplementary information.

Step 3: Add dependencies

Each component has it's own set of dependencies, because different components might have conflicting dependencies.

base images

For your convenience we have created several base images that can be used for python or R scripts. These images can be found in the OpenProblems Docker repository. Click on the packages to view the url you need to use. You are not required to use these images but install the required packages to make sure OpenProblems works properly.

• openproblems/base_python Base image for python scripts.

• openproblems/base_r Base image for R scripts.

• openproblems/base_pytorch_nvidia Base image for scripts that use pytorch with nvidia gpu support.

• openproblems/base_tensorflow_nvidia Base image for scripts that use tensorflow with nvidia gpu support.

custom image

Update the setup definition in the platforms section of the config file. This section describes the packages that need to be installed in the Docker image and are required for your method to run.

If you're using a custom image use the following minimum setup:

Please check out this guide for more information on how to add extra package dependencies.

viash run src/methods/my_python_method/config.vsh.yaml -- \
  ---setup cachedbuild

#| echo: false
viash run src/methods/my_python_method/config.vsh.yaml -- \
  ---setup cachedbuild

:::

Step 4: Edit script

A component's script typically has five sections:

a. Imports and libraries b. Argument values c. Read input data d. Generate results e. Write output data to file

This is what the script generated by the create_component component looks like:

The required sections are explained here in more detail:

a. Imports and libraries

In the top section of the script you can define which packages/libraries the method needs. If you add a new or different package add the dependency to config.vsh.yaml in the setup field (see above).

b. Argument block

The Viash code block is designed to facilitate prototyping, by enabling you to execute directly by running python script.py (or Rscript script.R for R users). Note that anything between "VIASH START" and "VIASH END" will be removed and replaced with a CLI argument parser when the components are being built by Viash.

Here, the par dictionary contains all the arguments defined in the config.vsh.yaml file (including those from the defined __merge__ file). When adding a argument in the par dict also add it to the config.vsh.yaml in the arguments section.

c. Read input data

This section reads any input AnnData files passed to the component.

d. Generate results

This is the most important section of your script, as it defines the core functionality provided by the component. It processes the input data to create results for the particular task at hand.

e. Write output data to file

The output stored in a AnnData object and then written to an .h5ad file. The format is specified by the API file specified in the __merge__ field in the config file.

Step 5: Add resources (optional)

It is possible to add additional resources such as a file containing helper functions or other resources. Please visit this page for more information on how to do this.

Step 6: Try component

Your component's API file contains the necessary unit tests to check whether your component works and the output is in the correct format.

You can test your component by using the following command:

viash test src/methods/my_python_method/config.vsh.yaml

#| echo: false
# use logistic_regression instead of 'my_python_method' because the script won't work.
# maybe copy a 'working' script here
viash test src/methods/logistic_regression/config.vsh.yaml

Visit "Run tests" for more information on running unit tests and how to interpret common error messages.

You can also run your component on local files using the viash run command. For example:

viash run src/methods/my_python_method/config.vsh.yaml -- \
  --input_train resources_test/task_template/cxg_mouse_pancreas_atlas/train.h5ad \
  --input_test resources_test/task_template/cxg_mouse_pancreas_atlas/test.h5ad \
  --output output.h5ad

Next steps

If your component works, please create a pull request.