BaseSpace Clarity LIMS v6.0 Release Notes

These Release Notes describe the key changes made to software components for BaseSpace Clarity LIMS since version 5.4.

When upgrading from a version prior to v5.4, review the release notes for v5.4 for a list of features and bug fixes introduced in that version.

Clarity LIMS v6 is deployable in both cloud hosted and on-premise environments.

New Features

Technology updates—An up-to-date technical stack ensures continued reliability, improved speed and capacity, and optimized system performance. For a complete list of updates, refer to the Appendix.
Project level automation—Users can now write custom scripts and perform custom actions on submitted samples. These custom actions can be triggered manually from the Projects & Samples screen.
Performance improvements—Improvements to the overall performance of Clarity LIMS v6 and to the existing API endpoints. A complete list of enhancements is provided in the Appendix.
Support for on-premise customers—Clarity LIMS v6 supports on-premise deployment renewals at launch. Contact your local sales specialist for more information.
ICA integration—Wet lab data can now be made available to data analysis pipelines via step level scripts.

Defect Repairs

An Elasticsearch error is no longer generated when date-formatted text is entered in a non-date field type.
Resolved an issue where controls were added to more workflows than samples processed in a step.
An API call to the reagent lot endpoint no longer fails when the lot status is expired automatically by the Clarity LIMS system.
Resolved inconsistent behavior on archived controls and deleted instrument types in Manifest and XML configuration slice files.
The root artifact name no longer reverts to default when updates to submitted sample details are submitted via automation.
Executing the Processes API endpoint on projects with over 500 samples and with a project name filter no longer returns an incomplete set of data.
A completed workflow stage is no longer missing from the Artifacts API endpoint if the previous step was not an output step.
Queue screen page load performance has been optimized.
Users no longer experience decreased performance associated with the Queue API making too many calls.
Users no longer experience decreased performance when loading Previous Step queue grouping.
Users no longer experience decreased performance when grouping types on Ice Bucket screen.
Dropdown fields that do not allow custom entries and have first option set as default are no longer silently applied to various API endpoints and sample sheet upload.
The changeWorkflow script no longer fails when processing 1152 derived samples.
Naming syntax LIST option now permits a combination of letters and numbers.
Master step configuration can now be updated when there is a comma in the naming convention.

Known Issues

There are no known issues at this time.

Additional Notes

Clarity LIMS v4.x is no longer supported by Illumina.
Clarity LIMS v6 does not support Oracle database. Illumina will continue to support v5.2 for on-premise customers requiring Oracle.
Clarity LIMS v6 does not support the Reporting module.
Clarity LIMS v6 has been reviewed for log4j vulnerabilities. All potential vulnerabilities have been addressed.

For questions or assistance, contact the Illumina Support team.


Technical Update Details


Clarity LIMS v5.4.0

Clarity LIMS v6.0.0





Oracle JDK 8u202

AdoptOpenJDK 8u292

RabbitMQ Server



Tomcat Application Server



Grails Web Framework



PostgreSQL Database



Performance Details

The overall performance of the Clarity LIMS system has been optimized on the following screens/actions:
Sample accessioning
Assigning samples to workflow
Removing samples from workflow
Queue screen page load
Ice Bucket screen load and loading of all grouping types
Adding labels to samples
Record Details screen
Next Steps screen
Search indexing
List of API endpoints with enhanced performance is as follows.
POST /api/{version}/samples/batch/retrieve
POST /api/{version}/samples/batch/create
POST /api/{version}/route/artifacts
POST /api/{version}/artifacts/batch/update
POST /api/{version}/artifacts/batch/retrieve
PUT /api/{version}/steps/{limsid}/actions
GET /api/{version}/steps/{limsid}/actions
POST /api/{version}/steps
GET /api/{version}/steps/{limsid}/details
GET /api/{version}/queues/{protocolStepId}
POST /api/{version}/steps/{limsid}/advance