Pipelines is based on Cromwell and WDL

Cromwell is an open-source Broad Institute based tool that is a Workflow Management System for bioinformatics. The language that is used to write the “tasks” for Cromwell is called the Workflow Description Language (WDL or pronounced as wee-dle): a human readable language for data processing workflows.

The basic Cromwell workflow consists of the Workflow which is the main driver of your pipeline; Tasks which include how your input is processed either in files parsed in or strings/other data types; Output which are how your processed output is processed out in files or strings/other data types.

For more information on how Cromwell functions and works, the documentation website is very well curated and can be found here with the GitHub repository (that also contains the link to the community forum) can be found here.

All commands and and runtime parameters would be written in WDL where syntax definitions and descriptions can be found here.

Note: When running a workflow in Cromwell, you will usually be submitting two files which are the .wdl and .json file where the .wdl file will contain the basic Cromwell workflow written in WDL whereas the .json file will point to the input and output files/strings/data types that will be parsed through your workflow. The subsequent subsections here will explore how to run basic and genetics applications specific pipelines.