Integration Properties Details
Last Updated: July 2024
This section describes the integration properties. For the integration packages listed below, unless otherwise specified, the properties are now in database. Database properties can be configured via omxProps-ConfigTool utility. From Clarity v6.3 and onwards, some properties are also configurable via System Setting.
iScan (v1.2.0 and onwards)
The iScan integration uses the SIS core service. Refer to SIS Core for common properties of the SIS core service.
NextSeq 500/550 (v2.4.0 and onwards)
¹ It is possible to configure support for multiple, identical seqservice.netPathPrefixSearch property values. Additional properties, each with the 99 suffix appended to their name, are also installed and intended for use by the Clarity LIMS Support team in automated validation tests. Those properties are not listed in the table.
NextSeq 1000/2000 (v2.5.0 and onwards)
NextSeq 1000/2000 integration uses the SIS core service. Refer to SIS Core for common properties of the SIS core service.
NextSeq 1000/2000 On-Prem (v1.0.0 and onwards)
integration.nextseq1k2k-onprem.v1.sequenceStepBaseName
integration.nextseq1k2k-onprem.v1.demultiplexStepBaseName
integration.nextseq1k2k-onprem.v1.analysis.metricsFilesToZip
integration.nextseq1k2k-onprem.v1.sampleSheetDir
NovaSeq 6000 File-Based (v2.6.0 and onwards)
¹ This version of the integration only supports a single active search-replace pair of each type: sampleSheetPathPrefixSearchReplaceSuffixes and netPathPrefixSearchReplaceSuffixes must each contain a single number, rather than a comma-separated list of numbers.
MiSeq (v8.3.0 and onwards)
Sequencing runs are matched using the reagent cartridge ID and the base name of the sequencing step.
You can configure support for multiple identical seqservice.netPathPrefixSearch property values. The integration also installs several additional properties, each with the 99 suffix appended to their name, that are not listed in the table. These properties are intended for use by the Clarity LIMS support team in automated validation tests. For more information, refer to Configure Multiple Identical netPathPrefixSearch Values.
MiSeq Dx (v1.11.0 and onwards)
The following table lists the properties installed with the Illumina MiSeqDx Integration Package. The following constraints are present when using the properties:
Sequencing runs are matched using the flow cell ID and the base name of the sequencing step – MiSeqDx Run (MiSeqDx).
Do not change this name – it is expected by the sequencing service that captures instrument run results. The base name is stored in the sequenceProcessBaseName property. If this name is changed without the property being updated, the 'flow cell ID <-> sequencing step base name' matching system will fail.
If necessary, you may modify the step name by editing or adding to the text after the base name portion. This part of the text is not used in the matching system. For example, you could change MiSeqDx Run (MiSeqDx) 1.2 to MiSeqDx Run (MiSeqDx) v1.2.
It is possible to configure support for multiple, identical seqservice.netPathPrefixSearch property values. Several additional properties, each with the ‘99’ suffix appended to their name, are also installed. These properties are intended for use by the Clarity LIMS support team in automated validation tests and are not listed in the table. For details, refer to Configure Multiple Identical netPathPrefixSearch Values.
Sequencer-API (v2.7.0 and onwards)
NovaSeq 6000 API-based and NovaSeq 6000 Dx integrations use the Sequencer-API integration service.
The application.yml file is at
All properties are configured automatically during installation, but they can also be configured by editing the application.yml file and then restarting Tomcat.
Properties in application.yml
Properties in Database
SIS Core (v2.6.0 and onwards)
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