General Orientation

LMAS code is in two repositories: source repository and report repository.

LMAS repository

This repository contains the code for LMAS workflow. The workflow is developed in Nextflow. The main file is LMAS.nf, to be executed by Nextflow.

Configuration

The main configuration file is nextflow.config and contains the main configuration parameters for the execution of LMAS. The parameters, containers and resources configuration files, that can be altered by the user to adapt LMAS execution, are params.config, containers.config, and resources.config, respectively.

Information on how to adjust these values is available here.

Templates

The templates folder contains the custom python scripts used by LMAS to process the data and compute the evaluation metrics, and are called in the LMAS.nf file.

Resources

The resources folder contains the compiled source code for the LMAS report. The report code is available in the report repository.

Lib

The lib folder contains custom Groovy code used by LMAS for the --help function.

Docker

The dockerfile for the main LMAS container, including all necessary python dependencies for the custom code in the templates is available in the docker folder

LMAS report

This repository. contains the source code for the interactive report that comes pre-packaged with LMAS. This project uses npx webpack to compile a standalone main.js file that is integrated into LMAS. The necessary dependencies for the project are provided in the environment.yml file available in this repo.