Collection of Fred Hutch-developed workflow configurations for execution via Cirro
Workflow languages like WDL, Nextflow, and Snakemake can be used to automate batch analysis of datasets. They can help with:
- Organizing a collection of interconnected analysis steps
- Efficiently utilizing high-performance computing resources
- Granularly controlling the dependencies needed for individual tools
- Sharing with collaborators across institutions
One of the systems used at Fred Hutch data management and analysis is the Cirro Data Platform. This repository contains the Cirro configurations for a collection of workflows developed by Fred Hutch researchers. These configurations are used to present a graphical interface for each workflow so that it can be run via the Cirro web interface.
The components of each workflow configuration are:
- Interactive form for the user to provide inputs (e.g. selecting a reference genome)
- Workflow input setup file, which references items from the form
- (optional) Pre-processing script used for any more complex logic needed to format workflow inputs
- (optional) Computational configuration passed to the workflow executor
- (optional) Output file configuration used for web-native visualizations
For more information, read the Cirro documentation on configuring workflows.
To contribute a new workflow to this repository, simply make a fork and open a pull request.