AWS HealthOmics variant stores and annotation stores will no longer be open to new customers starting November 7th, 2025. If you would like to use variant stores or annotation stores, sign up prior to that date. Existing customers can continue to use the service as normal. For more information, see AWS HealthOmics variant store and annotation store availability change.
Workflow definition files in HealthOmics
You use a workflow definition to specify information about the workflow, runs, and the tasks in the runs. You create workflow definitions in one or more files using a workflow definition language. HealthOmics supports workflow definitions written in WDL, Nextflow, or CWL. For details about each of these languages, see the language-specific detailed sections below.
You specify the following types of information in the workflow definition:
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Language version – The language and version of the workflow definition.
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Compute and memory – The compute and memory requirements for tasks in the workflow.
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Inputs – Location of the inputs to the workflow tasks. For more information, see HealthOmics run inputs.
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Outputs – Location to save the outputs that the tasks generate.
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Task resources – Compute and memory requirements for each task.
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Accelerators – other resources that the tasks require, such as accelerators.
