cromwell-bayesian-model-covid

This project demostrates running a Bayesian Covid model using Cromwell, Python, and Docker.

Cromwell:

Cromwell is an open-source Workflow Management System for bioinformatics.

Model:

Bayesian compartmental models for COVID-19: This repository contains code for Bayesian estimation of compartmental models for COVID-19 using python, numpyro and jax.

Execution:

Pre-requisites:

1. JAVA must be installed and be a minimum version of 11.
2. Docker must also be installed and running.

Please note: The cromwell workflow script will check for these requirements and stop execution if they are not met.

Input parameters:

Edit modelWorkflow_inputs.json file to specify the run parameters for the model.

First specify the name of the run for the model (do not include spaces).
For Bayesian, provide state, start_date and end_date.\

All other input parameters specify the model particulars, such as git repository, output folder of the model, types of output produced, installation and run scripts.

{
  "modelWorkflow.name_of_this_model_run": "bayesian",
  "modelWorkflow.state_array": ["GA"],
  "modelWorkflow.start_date_array": ["2020-03-05"],
  "modelWorkflow.end_date_array": ["2020-03-07"],
  "modelWorkflow.model_git_repository": "https://github.com/midas-network/bayesian-covid-model-demo.git",
  "modelWorkflow.model_output_folder": "bayesian-covid-model-demo/scripts/results",
  "modelWorkflow.model_output_file_types": "[npz,txt,png]",
  "modelWorkflow.install_model_script": "./scripts/sh/bayesian/install_model.sh",
  "modelWorkflow.run_model_script": "./scripts/sh/bayesian/run_model.sh",
  "modelWorkflow.model_runtime_docker": "python:3.6.15-bullseye",

  "modelWorkflow.setup_os_script": "./scripts/sh/setup_os.sh",
  "modelWorkflow.clone_repository_script": "./scripts/sh/clone_git_repository.sh",
  "modelWorkflow.copy_cromwell_logs_script": "./scripts/sh/copy_cromwell_logs.sh",
  "modelWorkflow.copy_model_output_script": "scripts/python/copy_model_output.py"
}

To execute:

1. From the command line execute the Cromwell workflow

./cromwell_workflow.sh

Results:

Results will be inside the model_output folder of this project:

~/../cromwell-bayesain-model-covid/model_output