Running Workflows

In the last few years there has been significant renewed interest in using a workflow approach to perform data analysis on Genomic, RNASeq, Proteomic and other types of data driven by the growth in big data and the popularity of cloud technologies ability for scalable storage and computing.

Scientific workflows have emerged to manage and describe the complexity that arises in scientific experiments, as well as data analysis and data processing. Complex workflows are created by linking or chaining several components or tasks into a pipeline.

A complete scientific workflow system requires first a clearly defined language and grammar which can be used to describe a workflow. Given a clearly specified workflow, a “workflow runner” of some sort is necessary in order to be able to actually run the workflow. A “runner” generally implements the following “roles”: a master or administrator, a scheduler, a task executor, and workers: in which the master receives and parses workflow document(s) and communicates requirements to the scheduler; the scheduler is typically trying to optimize usage of the available workers based on the requirements of the master(s), the executor causes tasks to be run on the specified schedule, and the workers do the work.

Out of this demand for scientific workflows have emerged several competing description languages such as the CWL (Common Workflow Language), WDL (Workflow Description Language), and NextFlow to name a few. These languages underwent rapid development and changes in the beginning and now are becoming more stable for use in production environments. Coupled with these languages are runner implementations such as cwltool, rabix, toil, and cromwell and new API standards such as GA4GH’s Task Execution Schema (TES) and the Workflow Execution Schema (WES). With the advent of so many choices; all under rapid development and at various stages of completeness its challenging to make a choice on any one technology.

ISB CGC’s approach therefore has been not to make a choice but to instead enable as many of these technologies as possible through documentation, support, and where necessary infrastructure.

As an alternative to workflows, we also recommend users consider dsub, an command-line tool that uses Docker to make it easy to submit and run single commands or batch scripts in the cloud. The dsub program is loosely based off of more traditional HPC systems such as Grid Engine or PBS where you “submit” your commands to a job scheduler that manages the compute resources, file I/O, and process execution.

More information on dsub and examples of its usage can be found at:


Have feedback or corrections? Please email us at feedback@isb-cgc.org.