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.
HealthOmics supports the following choices for WDL workflow definitions:
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WDL – Provides a spec-conformant WDL engine.
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WDL lenient – Designed to handle workflows migrated from Cromwell. It supports customer Cromwell directives and some non-conformant logic. For details, see Implicit type conversion in WDL lenient.
For information about each of the workflow 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.
