Integration Properties Details
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Clarity LIMS Software
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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.
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
The iScan integration uses the SIS core service. Refer to 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:
integration.iscan.v1.supportedImagingWorkflowStepNamePattern
The regex pattern for imaging step name which is supported by iScan integration.
Used by integration service.
Default:
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
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:
Do not modify the properties in this list:
integration.miseq.v8.seqservice.runReportViewsVersion
integration.miseq.v8.seqservice.synchronizationPeriod
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:
Do not modify the properties in this list:
integration.miseqdx.seqservice.runReportViewsVersion
integration.miseqdx.seqservice.synchronizationPeriod
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
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:
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:
integration.illuminaRunManager.miseqi100series.workflowNamePattern
The regex pattern for MiSeq i100 Series workflow name.
Default:
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
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:
Do not modify the properties in this list:
integration.nextseq.v2.seqservice.runReportViewsVersion
integration.nextseq.v2.seqservice.synchronizationPeriod
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:
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
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:
Do not modify the properties in this list:
integration.nextseq1k2k-onprem.v1.maxRetryAttempts
integration.nextseq1k2k-onprem.v1.pollingInterval
integration.nextseq1k2k-onprem.v1.retryInterval
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
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:
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 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:
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:
integration.illuminaRunManager.novaseqxseries.workflowNamePattern
The regex pattern for NovaSeq X Series workflow name.
Default:
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
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
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
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.
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.
NextSeq 1000/2000 integration uses the SIS core service. Refer to for common properties of the SIS core service.