Integration Properties Details

Last Updated: December 2024

Document Version: 2

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.

Illumina Run Manager (IRM) (v1.0.0 and onwards)

Changes on Illumina Run Manager integration properties take effect upon updates and do not require restart of Clarity.

Property	Description	Configurable via System Setting
integration.illuminaRunManager.pns.disableTlsVerification	Disables SSL/TLS verification at Illumina Run Manager PNS when disableTlsVerification is set to true and enables it otherwise (false). Used by integration service Default: false	No
integration.illuminaRunManager.pns.privateCaFilePath	Absolute path of private certificate authority (CA) chain file in PEM format. Used by integration service	No

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.

Changes on iScan integration properties take effect upon updates and do not require restart of the SIS core service.

Properties that are configurable via System Setting

Property	Description
integration.iscan.v1.autoCompleteAnalysisWorkflow	Boolean flag to control on/off analysis workflow auto-completion if the analysis is successful. Used by integration service Default: true
integration.iscan.v1.autoCompleteWorkflow	Boolean flag to control on/off imaging run workflow auto-completion if the run is successful. Used by integration service. Default: true
integration.iscan.v1.autoCompleteWorkflowUponFailure	Boolean flag to control on/off imaging run workflow auto-completion if the run is failed Used by integration service Default: false
integration.iscan.v1.supportedAnalysisWorkflowStepNamePattern	The regex pattern for analysis step name which is supported by iScan integration. Used by integration service. Default: ^Invoke Infinium Analysis (.*)$
integration.iscan.v1.supportedImagingWorkflowStepNamePattern	The regex pattern for imaging step name which is supported by iScan integration. Used by integration service. Default: ^Image Infinium BeadChip on iScan (.*)$

Other properties installed by the integration:

Do not modify the properties in this list:

• integration.iscan.v1.ica.api.uri

• integration.iscan.v1.ica.scopes

• integration.iscan.v1.workgroupid

MiSeq (v8.3.0 and onwards)

Sequencing runs are matched using the reagent cartridge ID and the base name of the sequencing step.

Do not change the base name. The sequencing service that captures sequencing run results expects the name. The base name is stored in the sequenceProcessBaseName property. If the name is changed without the property being updated, the reagent cartridge ID <-> sequencing step base name matching system fails. If you need to rename the step, for example to add a version number, modify the text before or after the base name portion. This part of the name is not used in the matching system. For example, change MiSeq Run (MiSeq v3.2) to Demo-MiSeq Run (MiSeq v3.2)-Updated.

Changes on integration.miseq.v8.seqservice.sequenceProcessBaseName property take effect upon updates and do not require restart of the integration service. For all remaining properties, integration service has to be restarted for property changes to take effect.

Properties that are configurable via System Setting

Property	Description
integration.miseq.v8.seqservice.sequenceProcessBaseName	Sequencing master step base display name. Partial matching is used to look up the master step. This property is added/updated by Illumina Preset Protocols (IPP) during the workflow installation. Default: Sequencing master step name (e.g., MiSeq Run (MiSeq v3.2))

Other properties installed by the integration:

Modify these properties using /opt/gls/clarity/config/configure_extensions_miseq_sequencingservice-v8.sh:

• integration.miseq.v8.seqservice.eventFileDirectory.1

• integration.miseq.v8.seqservice.eventFileDirectory.99

• integration.miseq.v8.seqservice.eventFileDirectorySuffixes

• integration.miseq.v8.seqservice.ignoreUnmatchedContainerIds

• integration.miseq.v8.seqservice.ignoreUnmatchedContainerIdsWaitDays

• integration.miseq.v8.seqservice.netPathPrefixReplace.1

• integration.miseq.v8.seqservice.netPathPrefixReplace.99

• integration.miseq.v8.seqservice.netPathPrefixSearch.1

• integration.miseq.v8.seqservice.netPathPrefixSearch.99

• integration.miseq.v8.seqservice.netPathPrefixSearchReplaceSuffixes

Do not modify the properties in this list:

• integration.miseq.v8.seqservice.runReportViewsVersion

• integration.miseq.v8.seqservice.synchronizationPeriod

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.

Changes on integration.miseqdx.seqservice.sequenceProcessBaseName and integration.miseqdx.seqservice.variantCallingProcessBaseName properties take effect upon updates and do not require restart of the integration service. For all remaining properties, integration service must be restarted for property changes to take effect.

Properties that are configurable via System Setting

Property	Description
integration.miseqdx.seqservice.sequenceProcessBaseName	Sequencing master step base display name. Partial matching is used to look up the process type. Default: Sequencing master step name (e.g., MiSeqDx Run (MiSeqDx))
integration.miseqdx.seqservice.variantCallingProcessBaseName	Sequencing process type base display name. Partial matching is used to look up the process type. Default: Variant Calling (MiSeqDx)

Other properties installed by the integration:

Modify these properties using /opt/gls/clarity/config/configure_extensions_miseqdx_sequencingservice.sh

• integration.miseqdx.seqservice.eventFileDirectory.1

• integration.miseqdx.seqservice.eventFileDirectory.99

• integration.miseqdx.seqservice.eventFileDirectorySuffixes

• integration.miseqdx.seqservice.ignoreUnmatchedContainerIds

• integration.miseqdx.seqservice.ignoreUnmatchedContainerIdsWaitDays

• integration.miseqdx.seqservice.netPathPrefixReplace.1

• integration.miseqdx.seqservice.netPathPrefixReplace.99

• integration.miseqdx.seqservice.netPathPrefixSearch.1

• integration.miseqdx.seqservice.netPathPrefixSearch.99

• integration.miseqdx.seqservice.netPathPrefixSearchReplaceSuffixes

Do not modify the properties in this list:

• integration.miseqdx.seqservice.runReportViewsVersion

• integration.miseqdx.seqservice.synchronizationPeriod

MiSeq i100 Series Cloud (v1.0.0 and onwards)

Changes on MiSeq i100 Series (Cloud) integration properties take effect upon updates and do not require restart of the SIS core service.

Properties that are configurable via System Setting

Property	Description
integration.miseqi100series.v1.allowedSequencingContainerTypes	Supported container type(s) for the integration. Comma-delimited. Used by integration service. Default: MiSeq i100 Series Dry Cartridge
integration.miseqi100series.v1.autocompleteAnalysisStepOnFailure	When autocompleteAnalysisStepOnFailure is set to true, the integration service will automatically advance and complete the analysis step upon secondary analysis failure. Used by integration service. Default: false
integration.miseqi100series.v1.autocompleteSequencingStep	When autocompleteSequencingStep is set to true, the integration service will automatically advance and complete the sequencing step upon handling the sequencing complete event. Used by integration service. Default: true
integration.miseqi100series.v1.autocompleteSequencingStepOnFailure	When autocompleteSequencingStepOnFailure is set to true, the integration service will automatically advance, complete the sequencing step and remove the samples from the sequencing step workflow upon handling the sequencing complete event in the event of failure. Used by integration service. Default: false
integration.miseqi100series.v1.automatedAnalysisStepNames	Master step name(s) for automated analysis run tracking. Comma-delimited Used by integration service. Default: AUTOMATED - Analysis Run (MiSeq i100 Series Sequencing v1.0)
integration.miseqi100series.v1.automatedSequencingStepNames	Master step name(s) for automated sequencing run tracking. Comma-delimited Used by integration service. Default: AUTOMATED - Sequencing Run (MiSeq i100 Series Sequencing v1.0)
integration.miseqi100series.v1.dryCartridgeBarcodeRegex	Regular expression (Java) for validating Dry Cartridge serial barcode. Used by integration service. Default: SC[0-9]{7}-SC[0-9]

Other properties installed by the integration:

Do not modify the properties in this list:

• integration.miseqi100series.v1.bssh.api.uri

• integration.miseqi100series.v1.bssh.region

• integration.miseqi100series.v1.cloudAppSessionSlug

• integration.miseqi100series.v1.cloudDemuxStatsFileNameRegex

• integration.miseqi100series.v1.cloudDemuxStatsTopLevelDatasetRegex

• integration.miseqi100series.v1.ica.scopes

• integration.miseqi100series.v1.localAppSessionSlug

• integration.miseqi100series.v1.localDemuxStatsFileNameRegex

• integration.miseqi100series.v1.localDemuxStatsTopLevelDatasetRegex

• integration.miseqi100series.v1.maxWaitingTimeInSeconds

• integration.miseqi100series.v1.workgroupid

MiSeq i100 Series On-Prem (v1.0.0 and onwards)

Properties that are configurable via System Setting

Property	Description
integration.illuminaRunManager.miseqi100series.analysisAutocompleteOnFailure	Boolean flag to control integration should auto-complete analysis step if the run is failed. Default: false
integration.illuminaRunManager.miseqi100series.analysisStepPatterns	The regex pattern for AUTOMATED analysis step name. Default: AUTOMATED \- Analysis Run \(MiSeq i100 Series On-Prem Sequencing v[0-9]+\.[0-9]+\)
integration.illuminaRunManager.miseqi100series.sequencingAutocompleteOnFailure	Boolean flag to control integration should auto-complete sequencing step if the run is failed. Default: false
integration.illuminaRunManager.miseqi100series.sequencingStepPatterns	The regex pattern for AUTOMATED sequencing step name. Default: AUTOMATED \- Sequencing Run \(MiSeq i100 Series On-Prem Sequencing v[0-9]+\.[0-9]+\)
integration.illuminaRunManager.miseqi100series.workflowNamePattern	The regex pattern for MiSeq i100 Series workflow name. Default: MiSeq i100 Series On-Prem v[0-9]+\.[0-9]+

Other properties installed by the integration:

Do not modify the properties in this list:

• integration.illuminaRunManager.miseqi100series.analysisEndedRecipe

• integration.illuminaRunManager.miseqi100series.analysisStartedRecipe

• integration.illuminaRunManager.miseqi100series.handlerMaxAttempts

• integration.illuminaRunManager.miseqi100series.handlerMaxRetryIntervalInSeconds

• integration.illuminaRunManager.miseqi100series.handlerMinRetryIntervalInSeconds

• integration.illuminaRunManager.miseqi100series.sequencingEndedRecipe

• integration.illuminaRunManager.miseqi100series.sequencingStartedRecipe

• integration.illuminaRunManager.miseqi100series.supportedInstrumentTypes

NextSeq 500/550 (v2.4.0 and onwards)

Sequencing runs are matched using the reagent cartridge ID and the sequencing steps base name. Do not change the base name. The name 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 'reagent cartridge ID <-> sequencing step base name' matching system fails. If necessary, modify the step name by editing or adding text after the base name portion, as it is not used in the matching system. For example, change NextSeq 500/550 Run (NextSeq 500/550 v1.1) to NextSeq 500/550 Run (NextSeq 500/550 v1.1) v2.

Changes on integration.nextseq.v2.seqservice.sequenceProcessBaseName property take effect upon updates and do not require restart of the integration service. For all remaining properties, integration service has to be restarted for property changes to take effect.

Properties that are configurable via System Setting

Property	Description
integration.nextseq.v2.seqservice.sequenceProcessBaseName	Sequencing master step base display name. Partial matching is used to look up the master step. Default: Sequencing master step name (e.g. NextSeq 500/550 Run (NextSeq 500/550 v1.1))

Other properties installed by the integration:

Modify these properties using /opt/gls/clarity/config/configure_extensions_nextseq_sequencingservice.sh

• integration.nextseq.v2.seqservice.eventFileDirectory.1

• integration.nextseq.v2.seqservice.eventFileDirectory.99

• integration.nextseq.v2.seqservice.eventFileDirectorySuffixes

• integration.nextseq.v2.seqservice.ignoreUnmatchedContainerIds

• integration.nextseq.v2.seqservice.ignoreUnmatchedContainerIdsWaitDays

• integration.nextseq.v2.seqservice.netPathPrefixReplace.1

• integration.nextseq.v2.seqservice.netPathPrefixReplace.99

• integration.nextseq.v2.seqservice.netPathPrefixSearch.1

• integration.nextseq.v2.seqservice.netPathPrefixSearch.99

• integration.nextseq.v2.seqservice.netPathPrefixSearchReplaceSuffixes

Do not modify the properties in this list:

• integration.nextseq.v2.seqservice.runReportViewsVersion

• integration.nextseq.v2.seqservice.synchronizationPeriod

NextSeq 1000/2000 Cloud (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.

Changes on NextSeq 1000/2000 integration properties take effect upon updates and do not require restart of the SIS core service.

Properties that are configurable via System Setting

Property	Description
integration.nextseq1k2k.v2.allowedSequencingContainerTypes	Supported container type(s) for NextSeq 1000/2000 integration. Delimited by comma(,). Used by integration service. Default: NextSeq 1000/2000 Reagent Cartridge
integration.nextseq1k2k.v2.analysisStepNames	Master step name(s) for automated NextSeq 1000/2000 analysis run. Delimited by comma(,). Used by integration service for analysis run tracking. Default: Master step name for analysis run step (e.g., Demultiplexing (NextSeq 1000/2000 Sequencing v2.4))
integration.nextseq1k2k.v2.automatedStepNames	Master step name(s) for automated NextSeq 1000/2000 sequencing run Delimited by comma(,). Used by integration service for sequencing run tracking Default: Master step name for sequencing run step (e.g., AUTOMATED - Sequencing Run (NextSeq 1000/2000 Sequencing v2.4))
integration.nextseq1k2k.v2.reagentBarcodeRegex	Regular expression (Java) ⚠ It should be less strict than or as strict as the actual reagent barcode regex Used by integration service to validate if the container name is valid before processing the event. Default: [A-Z]{2}[0-9]{7}-[A-Z0-9]{4}

Other properties installed by the integration:

Do not modify the properties in this list:

• integration.nextseq1k2k.v2.analysis.metricsFilesToZip

• integration.nextseq1k2k.v2.bssh.api.uri

• integration.nextseq1k2k.v2.bssh.region

• integration.nextseq1k2k.v2.cloudAnalysisLocationPropertyName

• integration.nextseq1k2k.v2.cloudAppSessionSlugToMetricsDataset

• integration.nextseq1k2k.v2.cloudRunIdPropertyName

• integration.nextseq1k2k.v2.ica.api.uri

• integration.nextseq1k2k.v2.ica.scopes

• integration.nextseq1k2k.v2.localAppSessionSlugToMetricsDataset

• integration.nextseq1k2k.v2.maxWaitingTimeInSeconds

• integration.nextseq1k2k.v2.workgroupid

NextSeq 1000/2000 On-Prem (v1.0.0 and onwards)

Except for the following properties, property updates require the integration service to be restarted to take effect:

• integration.nextseq1k2k-onprem.v1.sequenceStepBaseName

• integration.nextseq1k2k-onprem.v1.demultiplexStepBaseName

• integration.nextseq1k2k-onprem.v1.analysis.metricsFilesToZip

• integration.nextseq1k2k-onprem.v1.sampleSheetDir

Property	Description	Configurable via System Setting
integration.nextseq1k2k-onprem-v1.analysis.metricsFilesToZip	The comma-separated list of files that the integration service compresses and zips for upload to the Demultiplexing step in Clarity LIMS. These files must be in the same directory as the Demultiplex_Stats.csv file (for example, /mnt/run_data/<run_name>/Analysis/1/Data/Reports). Used by integration service. Default: Adapter_Metrics.csv,Demultiplex_Stats.csv,Index_Hopping_Counts.csv,Quality_Metrics.csv,Top_Unknown_Barcodes.csv	No
integration.nextseq1k2k-onprem-v1.analysis.demultiplexStepBaseName	The substring that the integration service uses to find the semi-automated demultiplexing step. Used by integration service. Default: Demultiplexing (NextSeq 1000/2000 On-Prem	No
integration.nextseq1k2k-onprem-v1.analysis.sequenceStepBaseName	The substring that the integration service uses to find the automated sequencing run step. Used by integration service. Default: AUTOMATED - Sequencing Run (NextSeq 1000/2000 On-Prem	No
integration.nextseq1k2k-onprem-v1.sampleSheetDir	The location of the copied generated sample sheet. This location is the same as the sample sheet directory from Prerequisite 2: Clarity LIMS with NAS Share and Mount Points (Refer to Installation guide for the appropriate version of the integration). Used by automation script. Default: /mnt/sample_sheet	No

Other properties installed by the integration:

Modify these properties using /opt/gls/clarity/config/configure_nextseq1k2k_onprem.sh

• integration.nextseq1k2k-onprem-v1.runFolderParentDir

Do not modify the properties in this list:

• integration.nextseq1k2k-onprem.v1.maxRetryAttempts

• integration.nextseq1k2k-onprem.v1.pollingInterval

• integration.nextseq1k2k-onprem.v1.retryInterval

NovaSeq 6000 File-Based (v2.6.0 and onwards)

Changes on integration.novaseq.seqservice.sequenceProcessBaseName property take effect upon updates and do not require restart of the integration service. For all remaining properties, integration service must be restarted for property changes to take effect.

Property	Description
integration.novaseq.seqservice.sequenceProcessBaseName	Sequencing master step display name. Partial matching is used to lookup the process type. Default: AUTOMATED - NovaSeq Run

Other properties installed by the integration:

Do not modify the properties in this list:

• integration.novaseq.runSetupFolder

• integration.novaseq.sampleSheetPathPrefixReplace.1

• integration.novaseq.sampleSheetPathPrefixReplace.99

• integration.novaseq.sampleSheetPathPrefixSearch.1

• integration.novaseq.sampleSheetPathPrefixSearch.99

• integration.novaseq.sampleSheetPathPrefixSearchReplaceSuffixes

• integration.novaseq.seqservice.maximumRedeliveryAttempts

• integration.novaseq.seqservice.netPathPrefixReplace.1

• integration.novaseq.seqservice.netPathPrefixReplace.99

• integration.novaseq.seqservice.netPathPrefixSearch.1

• integration.novaseq.seqservice.netPathPrefixSearch.99

• integration.novaseq.seqservice.netPathPrefixSearchReplaceSuffixes

• integration.novaseq.seqservice.redeliveryDelay

• integration.novaseq.seqservice.synchronizationPeriod

NovaSeq X Series Cloud (v1.3.0 and onwards)

Changes on NovaSeq X Series (Cloud) integration properties take effect upon updates and do not require restart of the SIS core service.

Property	Description
integration.novaseqxseries.v1.allowedSequencingContainerTypes	Supported container type(s) for NovaSeq X Series (Cloud) integration. Delimited by comma(,). Used by integration service. Default: Library 2-tube Strip,Library 8-tube Strip
integration.novaseqxseries.v1.autocompleteAnalysisStepOnFailure	When autocompleteAnalysisStepOnFailure is set to true, the integration service will automatically advance and complete the analysis step upon secondary analysis failure. Used by integration service. Default: false
integration.novaseqxseries.v1.autocompleteSequencingStep	When autocompleteSequencingStep is set to true, the integration service will automatically advance and complete the sequencing step upon handling the sequencing complete event. Used by integration service. Default: true
integration.novaseqxseries.v1.autocompleteSequencingStepOnFailure	When autocompleteSequencingStepOnFailure is set to true, the integration service will automatically advance, complete the sequencing step and remove the samples from the sequencing step workflow upon handling the sequencing complete event in the event of failure. Used by integration service. Default: false
integration.novaseqxseries.v1.automatedAnalysisStepNameRegex	The regex of Master step name for automated NovaSeq X Series analysis run Default: ^AUTOMATED - Analysis Run (NovaSeq X Series Sequencing v[0-9]+.[0-9]+)$
integration.novaseqxseries.v1.automatedSequencingStepNameRegex	The regex of Master step name for automated NovaSeq X Series sequencing run Default: ^AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v[0-9]+.[0-9]+)$
integration.novaseqxseries.v1.libraryTubeStripRegex	Regular expression (Java) ⚠ It should be less strict than or as strict as the actual library tube strip barcode regex Used by integration service to validate if the container name is valid before processing the event. Default: [A-Za-z]{2}[0-9]{7}-[A-Za-z0-9]{3}

Other properties installed by the integration:

Do not modify the properties in this list:

• integration.novaseqxseries.v1.bssh.api.uri

• integration.novaseqxseries.v1.bssh.region

• integration.novaseqxseries.v1.cloudAppSessionSlug

• integration.novaseqxseries.v1.cloudDemuxStatsFileNameRegex

• integration.novaseqxseries.v1.cloudDemuxStatsTopLevelDatasetRegex

• integration.novaseqxseries.v1.cloudHighLevelSummaryFileNameRegex

• integration.novaseqxseries.v1.cloudHighLevelSummaryTopLevelDatasetRegex

• integration.novaseqxseries.v1.ica.api.uri

• integration.novaseqxseries.v1.ica.scopes

• integration.novaseqxseries.v1.localAppSessionSlug

• integration.novaseqxseries.v1.localDemuxStatsFileNameRegex

• integration.novaseqxseries.v1.localDemuxStatsTopLevelDatasetRegex

• integration.novaseqxseries.v1.localHighLevelSummaryFileNameRegex

• integration.novaseqxseries.v1.localHighLevelSummaryTopLevelDatasetRegex

• integration.novaseqxseries.v1.maxWaitingTimeInSeconds

• integration.novaseqxseries.v1.workgroupid

NovaSeq X Series On-Prem (v1.0.0 and onwards)

NovaSeq X Series On-Prem integration requires installation of IRM integration service. Changes on NovaSeq X Series (On-Prem) integration properties take effect upon updates and do not require restart of the IRM integration service.

Properties that are configurable via System Setting

Property	Description
integration.illuminaRunManager.novaseqxseries.analysisAutocompleteOnFailure	When analysisAutocompleteOnFailure is set to true, the integration service will automatically advance and complete the analysis step upon secondary analysis failure. Used by integration service. Default: false
integration.illuminaRunManager.novaseqxseries.analysisStepPatterns	The regex pattern for AUTOMATED analysis step name. Default: AUTOMATED \- Analysis Run \(NovaSeq X Series On-Prem Sequencing v[0-9]+\.[0-9]+\)
integration.illuminaRunManager.novaseqxseries.sequencingAutocompleteOnFailure	When sequencingAutocompleteOnFailure is set to true, the integration service will automatically advance, complete the sequencing step and remove the samples from the sequencing step workflow upon handling the sequencing complete event in the event of failure. Used by integration service. Default: false
integration.illuminaRunManager.novaseqxseries.sequencingStepPatterns	The regex pattern for AUTOMATED sequencing step name. Default: AUTOMATED \- Sequencing Run \(NovaSeq X Series On-Prem Sequencing v[0-9]+\.[0-9]+\)
integration.illuminaRunManager.novaseqxseries.workflowNamePattern	The regex pattern for NovaSeq X Series workflow name. Default: NovaSeq X Series On-Prem v[0-9]+\.[0-9]+

Other properties installed by the integration:

Do not modify the properties in this list:

• integration.illuminaRunManager.novaseqxseries.analysisEndedRecipe

• integration.illuminaRunManager.novaseqxseries.analysisStartedRecipe

• integration.illuminaRunManager.novaseqxseries.handlerMaxAttempts

• integration.illuminaRunManager.novaseqxseries.handlerMaxRetryIntervalInSeconds

• integration.illuminaRunManager.novaseqxseries.handlerMinRetryIntervalInSeconds

• integration.illuminaRunManager.novaseqxseries.sequencingEndedRecipe

• integration.illuminaRunManager.novaseqxseries.sequencingStartedRecipe

• integration.illuminaRunManager.novaseqxseries.supportedInstrumentTypes

Sequencer-API (v2.7.0 and onwards)

NovaSeq 6000 API-based and NovaSeq 6000 Dx integrations use the Sequencer-API integration service.

Changes on Sequencer-API properties take effect upon updates and do not require restart of the Clarity LIMS except for properties in application.yml file. The property names should not be modified.

The application.yml file is at

opt/gls/clarity/extensions/sequencer-api/*

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

Property	Description
spring.profiles.active	Tells the application that it is running deployed in Tomcat. Default: tomcat ⚠ Do not change
clarity.url	Base URL that the Sequencer API service uses to contact the Clarity LIMS. The installation script (configure_sequencer_api_application) prompts for this URL.
clarity.username	Username to be used when communicating with Clarity LIMS.
security.token-expiry	Specifies (in hours) the expiry period for login tokens issued by the Sequencer API. Default: 88

Properties in Database

Properties that are configurable via System Setting

Property	Description
integration.sequencer_api.v2.novaseq.sequenceStepNames	List of NovaSeq sequencing run step names for which the integration can find samples queued. Names must be an exact match to the name of the step in Clarity LIMS (not the master step/process type). Each line must be indented to the same point and start with a dash (-). Default: Sequencing run step names. Example given below. - "AUTOMATED - NovaSeq Run (NovaSeq 6000 v3.8)" - "AUTOMATED - NovaSeqDx Run (NovaSeqDx v1.1)"
integration.sequencer_api.v2.run.autoComplete	Determines whether the sequencing run step must be completed automatically after parsing the run metrics on a run along with run.autoCompleteOnlyAtSuccess. ℹ For more information, refer to Configuring autoComplete Properties section in Configuration guides for NovaSeq 6000 API-based or NovaSeq 6000Dx API-based integrations. Default: true
integration.sequencer_api.v2.run.autoCompleteOnlyAtSuccess	Determines which of the following options that the sequencing run step must be: Autocompleted when the run status is RunCompletedSuccessfully (if autoCompleteOnlyAtSuccess is true) Autocompleted regardless of the run status (if autoCompleteOnlyAtSuccess is false). ℹ For more information, refer to Configuring autoComplete Properties section in Configuration guides for NovaSeq 6000 API-based or NovaSeq 6000Dx API-based integrations. Default: true

Other properties installed by the integration:

Do not modify the properties in this list:

• app.oauth2.sequencer_api.signingKey

• integration.sequencer_api.v2.novaseq.flowcells

• integration.sequencer_api.v2.novaseq.reagents

• integration.sequencer_api.v2.novaseq.useReagentValidation

• integration.sequencer_api.v2.novaseq.useSerialNumberForReagentLotNumber

• integration.sequencer_api.v2.recipe.udfNames

• integration.sequencer_api.v2.recipe.sampleSheet.outputName

• integration.sequencer_api.v2.recipe.sampleSheet.notAvailableValue

• integration.sequencer_api.v2.run.stepUdfNames

• integration.sequencer_api.v2.run.metricUdfNames

SIS Core (v2.6.0 and onwards)

Do not modify the properties in this list:

• integration.sis.v2.maxNumberOfMessages

• integration.sis.v2.receiveMessageWaitTimeSeconds

• integration.sis.v2.maxMessageHandlingRetryTimes

• integration.sis.v2.sqsPollingInterval

In the event that the properties are updated, SIS core service must be restarted for updated property values to take effect.

Revision History

Version	Changes
2	Added properties of Illumina Run Manager, NovaSeq X Series (cloud and on-premise), MiSeq i100 Series (cloud and on-premise). Updated properties of existing integrations to only reflect details of properties that can be configured by user. Reordered sections in alphabetical order of integration.
1	Initial release.