kGWASflow Configuration

Initializing kGWASflow

To configure kGWASflow, you first need to initialize a new kGWASflow working directory by following the below steps:

# Activating the conda environment
conda activate kgwasflow

# Initializing a new kgwasflow working dir
kgwasflow init --working-dir path/to/your/work_dir 

or

# Activating the conda environment
conda activate kgwasflow

# Change into your preferred working directory
cd path/to/your/work_dir 

# Initializing a new kgwasflow working dir
kgwasflow init

kGWASflow Working Directory Structure

This command will initialize a new kGWASflow working directory with the default configuration files. Below is the directory structure of the working directory:

path/to/your/work_dir 
├── config
│   ├── config.yaml
│   ├── phenos.tsv
│   └── samples.tsv
└── test

kGWASflow Configuration Files

Below are the configuration files generated by kgwasflow init command:

• config/config.yaml is a YAML file containing the workflow configuration.

• config/samples.tsv is a TSV file containing the sample information.

• config/phenos.tsv is a TSV file contains the phenotype information.