cromwell-epispot

This project demostrates running Epispot using Cromwell, Python, and Docker.

Cromwell:

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

Model:

Epispot: A Python package for the mathematical modeling of infectious diseases via compartmental models.

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 Epispot, provide each start, stop, num_samples and pop_size.

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": "epispot",
  "modelWorkflow.start_array": [0],
  "modelWorkflow.stop_array": [50,100],
  "modelWorkflow.num_samples_array": [200,400],
  "modelWorkflow.pop_size_array": ["1.78e6"],
  "modelWorkflow.model_executable": "./scripts/python/epispot_run.py",
  "modelWorkflow.model_git_repository": "https://github.com/epispot/epispot",
  "modelWorkflow.model_output_folder": "results",
  "modelWorkflow.model_output_file_types": "[png,txt]",
  "modelWorkflow.install_model_script": "./scripts/sh/epispot/install_model.sh",
  "modelWorkflow.run_model_script": "./scripts/sh/epispot/run_model.sh",
  "modelWorkflow.model_runtime_docker": "python:3.9.18-slim-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-epispot/model_output