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.
⚠️ Changes on iScan integration properties take effect upon updates and do not require restart of the SIS core service.
Boolean flag to control on/off imaging run workflow auto-completion if the run is failed
Used by integration service
Default: false
Yes
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
Yes
integration.iscan.v1.ica.api.uri
Base URI for Illumina Connected Analytics integration.
Used by automation script to retrieve information.
Default: https://use1.platform.illumina.com
No
integration.iscan.v1.workgroupid
Workgroup ID for BaseSpace Sequence Hub and Illumina Connected Analytics integration.
Used by automation script
No
integration.iscan.v1.ica.scopes
(Optional) Scopes used by Illumina Connected Analytics for access control.
Delimited by comma(,).
Used by automation script.
No
NextSeq 500/550 (v2.4.0 and onwards)
ℹ️ 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.
ℹ️ 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.
The current version of the Run Report views in the database. The value 0 represents the state before the views are created. This property is automatically updated by the run report.
A flag indicating if event files that cannot be matched to reagent cartridges in Clarity LIMS should be archived after a certain time (true), or continually reprocessed (false).
Default: false
ℹ️ To prevent the gls_events file directory from becoming cluttered, it is recommended that the value of this property is set to true.
Determines how often the integration scans the run data folder to check if there is any new runs. synchronizationPeriod is in seconds.
Default: 60
No
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.
⚠️ Changes on NextSeq 1000/2000 integration properties take effect upon updates and do not require restart of the SIS core service.
Property
Description
Configurable via System Setting
integration.nextseq1k2k.v2.bssh.api.uri
Base URI for BaseSpace Sequence Hub integration.
Used by integration service to retrieve information from BaseSpace Sequence Hub during sequencing and analysis event handling
Run the configure BSSH bash script to update this property.
Default: https://api.basespace.illumina.com
No
integration.nextseq1k2k.v2.bssh.region
Region where BaseSpace Sequence Hub is located.
Used by integration service
Run the configure BSSH bash script to update this property.
Default: use1
No
integration.nextseq1k2k.v2.ica.api.uri
Base URI for Illumina Connected Analytics integration.
Used by automation script to retrieve information and to create planned run and v2 samplesheet.
Default: https://use1.platform.illumina.com
No
integration.nextseq1k2k.v2.workgroupid
Workgroup ID for BaseSpace Sequence Hub and Illumina Connected Analytics integration.
Used by automation script
No
integration.nextseq1k2k.v2.ica.scopes
(Optional) Scopes used by Illumina Connected Analytics for access control.
Delimited by comma(,).
Used by automation script.
No
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))
Yes
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))
The interval (in seconds) indicates how often the integration service checks for new files created in the Run parent directory (for example, a check for newly created files in the Run parent directory is done every 180 seconds).
Used by integration service.
Default: 180
No
integration.nextseq1k2k-onprem.v1.retryInterval
The interval (in seconds) that the integration service waits before trying to handle the event again when it encounters an error.
The number of additional times that the integration service tries to handle an event.
Used by integration service
Default: 4
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).
The location that the integration scans for new run folders to handle run events. This location is the same as the Run parent directory from Prerequisite 2: Clarity LIMS with NAS Share and Mount Points (Refer to Installation guide for the appropriate version of the integration).
ℹ️ 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.
The directory where the instrument control software or analysis software looks for sample sheets, typically a Windows path to a network drive. E.g., \nas\network\sample_sheet
Search and replace entries for transforming Windows to Linux network paths. This property must be set to the single SUFFIX used in the two previous properties.
Search and replace entries for transforming Windows to Linux network paths. This property must be set to the single SUFFIX used in the two properties above.
Default: 99
No
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.
⚠️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.
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))
The current version of the Run Report views in the database. The value 0 represents the state before the views are created. This property is automatically updated by the run report.
A flag indicating if event files that cannot be matched to reagent cartridges in Clarity LIMS should be archived after a certain period (true) or continually reprocessed (false).
Default: false
ℹ️ To prevent the gls_events file directory from becoming cluttered, it is recommended that the value of this property is set to true
Determines how often the integration scans the run data folder to check if there is any new runs. synchronizationPeriod is in seconds.
Default: 60
No
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.
⚠️ 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.
A flag indicating if event files that cannot be matched to flow cells in Clarity LIMS should be archived after a period of time (true), or continually reprocessed (false).
Default: false
ℹ️ To prevent the gls_events file directory from becoming cluttered, it is recommended that the value of this property is set to ‘true’.
The current version of the Run Report views in the database. The value 0 represents the state before the views are created. This property is automatically updated by the run report.
Sequencing process type base display name. Partial matching is used to look up the process type.
Default: Variant Calling (MiSeqDx)
Yes
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.
⚠️ 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
Property
Description
Configurable via System Setting
app.oauth2.sequencer_api.signingKey
Private key that is used when signing/validating OAuth tokens. Changing this key invalidates any issued tokens.
Configure whether or not serial number of Reagent will be mapped to lot number.
If false, lot number will be mapped to lot number
Default: false
No
integration.sequencer_api.v2.recipe.udfNames
Configures the names of the fields used in the run recipe.
Each value must be enclosed in quotes (e.g., integration.sequencer_api.v2.recipe.udfNames.runMode "Run Mode").
Value provided for sampleLoadingType must match the value provided in the run configuration (e.g., integration.sequencer_api.v2.recipe.udfNames.sampleLoadingType "Loading Workflow Type").
ℹ️ For more information, refer to the Run Recipe Contents section of NovaSeq 6000 Run in Configuration guides for NovaSeq 6000 API-based or NovaSeq 6000Dx API-based integrations.
Configures the name of the sample sheet file placeholder on the step where run recipe information is populated, and the property value to use when the file is not found.
No
integration.sequencer_api.v2.run.stepUdfNames
Configures the master step field names to be used when recording run results.
Each value must be enclosed in quotes (e.g., integration.sequencer_api.v2.run.stepUdfNames.runID "Run ID")
Value provided for sampleLoadingType must match the value provided in the run configuration (e.g., integration.sequencer_api.v2.run.stepUdfNames.sampleLoadingType "Loading Workflow Type"). It is expected that the run step field and the field on the input derived sample share a name.
ℹ️ For more information,
for NovaSeq 6000 API-based integrations, refer to Configuration guide (Master Step Fields section of Step 1: AUTOMATED - NovaSeq Run in Protocol 4: AUTOMATED - NovaSeq Run)
for NovaSeq 6000 Dx API-based integrations, refer to Configuration guide (Master Step Fields section of Step 1: AUTOMATED - NovaSeqDx Run in Protocol 4: AUTOMATED - NovaSeqDx Run)
No
integration.sequencer_api.v2.run.metricUdfNames
Configures the result file custom fields/measurement global field names to be used when recording run results. These fields capture the run data.
ℹ️ For more information,
for NovaSeq 6000 API-based integrations, refer to Configuration guide (Master Step Fields section of Step 1: AUTOMATED - NovaSeq Run in Protocol 4: AUTOMATED - NovaSeq Run)
for NovaSeq 6000 Dx API-based integrations, refer to Configuration guide (Master Step Fields section of Step 1: AUTOMATED - NovaSeqDx Run in Protocol 4: AUTOMATED - NovaSeqDx Run)
No
integration.sequencer_api.v2run.autoComplete
Determines whether the sequencing run step must be completed automatically after parsing the run metrics on a run along with run.autoCompleteOnlyAtSuccess.
ℹ️ For more information, refer to Configuring autoComplete Properties section in Configuration guides for NovaSeq 6000 API-based or NovaSeq 6000Dx API-based integrations.
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).
ℹ️ 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
Yes
SIS Core (v2.6.0 and onwards)
⚠️ SIS core service must be restarted for updated property values to take effect.
