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A method configuration or config is a table that lists, for a particular method, what inputs and parameter settings the workflow expects from you. Sometimes workflow authors will publish method configurations in the Method Repository to provide default values for others who may not know what values to use. You must enter values for required inputs, and you can enter values for optional inputs if you like (but you don't have to). The table also includes a list of the final outputs defined in the workflow.
In practice, there are three different ways to specify values for parameters and file inputs:
This written or video tutorial will teach you how to configure a method in a workspace.
For an example, see https://portal.firecloud.org/#workspaces/help-firecloud/FireCloud101-Basics/method-configs/gatk/HaplotypeCallerGvcfMc