Note: this page is under re-construction as we clean up our various components of documentation around workflow managers. Please pardon our dust or schedule a Data House Call with a staff member if you have questions about workflow managers.

Understanding Workflows

When performing bioinformatic analysis, scientists often need to perform a series of interconnected computational transformations of the raw input data. While it is possible to coordinate multiple tasks using BASH scripts or batch submission to a SLURM cluster, it can be far more convenient to use software which has been specifically designed to coordinate these types of workflows. Some examples of those workflow managers are:

Cromwell/WDL, and Nextflow.

Getting Started with WDL

You can find a wealth of information on getting started using WDL workflows at Fred Hutch on the Resource Library entry for WDL and on our PROOF page. PROOF is a tool that wraps the Cromwell workflow manager for use at Fred Hutch.

Getting Started with Nextflow

Check our our various Resource Library entries related to Nextflow workflows.

While there are many workflows developed by researchers around the world, the Data Core is also working to maintain a catalog of workflows for Fred Hutch researchers. If you have any questions about using these workflows, or if you run into any issues, the Data Core can help provide help with troubleshooting and enhancements as needed.

See the Nextflow Catalog for a list of existing workflows you can run.

For a longer list of workflows developed by the worldwide community of Nextflow developers, visit the nf-core workflow catalog.

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