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Run step using YAML config

It's possible to parametrise the functionality of a step using a YAML configuration file. This is useful when you want to run a step multiple times with different parameters or simply to avoid having to specify the same parameters every time you run a step.

Info

The package uses Hydra to handle configuration files. For more information, please visit the Hydra documentation.

To run a step using a configuration file, you need to create a configuration file in YAML format.

config/
├─ step/
│  └─ my_gwas_catalog_sumstat_preprocess.md
└─ my_config.yml

The configuration file should contain the parameters you want to use to run the step. For example, to run the gwas_catalog_sumstat_preprocess step, you need to specify the step.raw_sumstats_path and step.out_sumstats_path parameters. The configuration file should look like this:

defaults:
    - config
    - _self_

This config file will specify that your configuration file will inherit the default configuration (config) and everything provided (_self_) will overwrite the default configuration.

defaults:
    - gwas_catalog_sumstat_preprocess

raw_sumstats_path: /path/to/raw_sumstats
out_sumstats_path: /path/to/out_sumstats

This config file will inherit the default configuration for the gwas_catalog_sumstat_preprocess step and overwrite the raw_sumstats_path and out_sumstats_path parameters.

Once you have created the configuration file, you can run your own new my_gwas_catalog_sumstat_preprocess:

gentropy step=my_gwas_catalog_sumstat_preprocess --config-dir=config --config-name=my_config
  • 2024-01-12
  • 2025-01-22
  • Contributors
    • vivienho
    • web-flow
    • ireneisdoomed