NMDC Workflows

General Guidelines

NMDC aims to integrate existing open-source bioinformatics tools into standardized workflows for processing raw multi-omics data to produce interoperable and reusable annotated data products. Any commercial software are optional alternatives and not required.

Execution Environment

Two common ways to install and run the NMDC workflows:

• Native installation

• Containers

The NMDC workflows have been written in WDL and require a WDL-capable Workflow Execution Tool (i.e., Cromwell). To ease the native installation, Docker images have been created for the third-party tools for all of the workflows as well. The workflows use the corresponding Docker images to run the required third-party tools. Databases must be downloaded and installed for most of the workflows.

The NMDC workflows are also available as a web application called NMDC EDGE. The application has only the NMDC workflows integrated into an updated framework for EDGE Bioinformatics; this provides the workflows, third-party software, and requisite databases within a platform with a user-friendly interface. NMDC EDGE is provided as a web application especially for users who are not comfortable with running command line tools or without the computational resources to run the command line/Docker versions.