CWL
ICA supports running pipelines defined using Common Workflow Language (CWL).
Compute Type
To specify a compute type for a CWL CommandLineTool, use the ResourceRequirement
with a custom namespace.
Reference Compute Types for available compute types and sizes.
The ICA Compute Type will be determined automatically based on CWL ResourceRequirement coresMin/coresMax (CPU) and ramMin/ramMax (Memory) values using a "best fit" strategy to meet the minimum specified requirements (refer to the Compute Types table).
For example, take the following ResourceRequirements
:
This would result in a best fit of standard-large
ICA Compute Type request for the tool.
If the specified requirements can not be met by any of the presets, the task will be rejected and failed.
FPGA requirements can not be set by means of CWL ResourceRequirements.
The Machine Profile Resource in the graphical editor will override whatever is set for requirements in the ResourceRequirement.
Considerations
If no Docker image is specified, Ubuntu will be used as default. Both : and / can be used as separator.
CWL Overrides
ICA supports overriding workflow requirements at load time using Command Line Interface (CLI) with JSON input. Please refer to CWL documentation for more details on the CWL overrides feature.
In ICA you can provide the "override" recipes as a part of the input JSON. The following example uses CWL overrides to change the environment variable requirement at load time.
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