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.
⚠️ Changes on iScan integration properties take effect upon updates and do not require restart of the SIS core service.
Property
Description
Configurable via System Setting
integration.iscan.v1.supportedImagingWorkflowStepNamePattern
The regex pattern for imaging step name which is supported by iScan integration.
Used by integration service.
Default:
Yes
integration.iscan.v1.supportedAnalysisWorkflowStepNamePattern
The regex pattern for analysis step name which is supported by iScan integration.
Used by integration service.
Default:
Yes
integration.iscan.v1.supportedBeadChipProductTypes
The supported product types to iLASS-defined container name mapping.
Key = Beadchip Product Type Name (e.g., GDA_PGx-8v1-0)
Value = iLASS-defined container name (e.g., Infinium Genotyping with PGx Array LCG-8)
Key-value separator =
->Key-value delimiter = ,
Used by integration service
Default:
Yes
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
Yes
integration.iscan.v1.autoCompleteWorkflowUponFailure
ul>
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.
Property
Description
Configurable on System Setting
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))
Yes
integration.nextseq.v2.seqservice.eventFileDirectory.1
A network location monitored for event files (e.g., /mnt/illumina/gls_events/)
Default: /mnt/gls_events
No
integration.nextseq.v2.seqservice.netPathPrefixSearch.1¹
The network directory prefix contained in the event file - most likely in Windows format.
Default: \nas\network\run_data
No
integration.nextseq.v2.seqservice.netPathPrefixReplace.1
The mapped network directory mount name on the server used to access the run data directory (e.g., /mnt/network/data)
Default: /mnt/run_data
No
integration.nextseq.v2.seqservice.eventFileDirectorySuffixes
A list of eventFileDirectory path entries to monitor for event files. The value is one or more comma-separated integers.
Default: 99
ℹ️ Configured on install to point to 1.
No
integration.nextseq.v2.seqservice.netPathPrefixSearchReplaceSuffixes
A list of netPathPrefix search and replace entries for transforming Windows to Linux network paths. The value is one or more comma-separated integers.
Default: 99
ℹ️ Configured on install to point to 1.
No
integration.nextseq.v2.seqservice.runReportViewsVersion
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.
Default: 0
No
integration.nextseq.v2.seqservice.ignoreUnmatchedContainerIds
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.
No
integration.nextseq.v2.seqservice.ignoreUnmatchedContainerIdsWaitDays
The number of days between when the event is created and the event file is archived.
Default: 14
No
integration.nextseq.v2.seqservice.synchronizationPeriod
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))
Yes
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
Yes
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:
Yes
integration.nextseq1k2k.v2.maxWaitingTimeInSeconds
Maximum wait time including retry time (in seconds) for integration to retrieve a file from BaseSpace Sequence Hub.
Used by integration service.
Default: 10800
No
integration.nextseq1k2k.v2.cloudRunIdPropertyName
Name of BaseSpace Sequencer Hub run property that contains Cloud run ID.
Used by integration service.
Default: BaseSpace.Cloud.Run.Id
No
integration.nextseq1k2k.v2.cloudAnalysisLocationPropertyName
Name of BaseSpace Sequence Hub run property that contains Cloud analysis location.
Used by integration service.
Default: Cloud.Analysis.Location
No
integration.nextseq1k2k.v2.localAppSessionSlugToMetricsDataset
Key-value map for Local analysis tracking
Key = the BaseSpace Sequence Hub application slug filter
Value = associated metrics dataset name
Key-value separator =
->Key-value delimiter = ,
Used by integration service
Default:
No
integration.nextseq1k2k.v2.cloudAppSessionSlugToMetricsDataset
Key-value map for Cloud analysis tracking
Key = the BaseSpace Sequence Hub application slug filter
Value = associated metrics dataset name
Key-value separator =
->Key-value delimiter = ,
Used by integration service
Default:
No
integration.nextseq1k2k.v2.analysis.metricsFilesToZip
The list of analysis metric files in the Reports folder to be zipped and uploaded to the Demultiplexing step
Delimited by comma(,)
Default: Adapter_Metrics.csv,Demultiplex_Stats.csv,Index_Hopping_Counts.csv,Quality_Metrics.csv,Top_Unknown_Barcodes.csv
No
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.pollingInterval
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.
Used by integration service.
Default: 180
No
integration.nextseq1k2k-onprem.v1.maxRetryAttempts
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).
Used by automation script.
Default: /mnt/sample_sheet
No
integration.nextseq1k2k-onprem-v1.runFolderParentDir
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).
Used by integration service.
Default: /mnt/run_data
No
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.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
Yes
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
Yes
NovaSeq 6000 File-Based (v2.6.0 and onwards)
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.
Property
Description
Configurable on System Setting
integration.novaseq.seqservice.sequenceProcessBaseName
Sequencing master step display name. Partial matching is used to lookup the process type.
Default: Master step name for sequencing step (e.g., AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.3))
Yes
integration.novaseq.seqservice.synchronizationPeriod
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
integration.novaseq.seqservice.redeliveryDelay
Controls the rate (in seconds) in which additional attempts to process run folder will occur for error events.
Default: 180
No
integration.novaseq.seqservice.maximumRedeliveryAttempts
Determines the number of additional attempts to process run folder for error events.
Default: 4
No
integration.novaseq.runSetupFolder
The directory where the run recipe files are written. E.g., /mnt/run_setup
Default: /mnt/run_setup
No
integration.novaseq.sampleSheetPathPrefixSearch.SUFFIX
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
Default: \nas\network\sample_sheet
No
integration.novaseq.sampleSheetPathPrefixReplace.SUFFIX
The directory where the sample sheets are written. E.g., /mnt/sample_sheet
Default: /mnt/sample_sheet
No
integration.novaseq.sampleSheetPathPrefixSearchReplaceSuffixes¹
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.
Default: 99
No
integration.novaseq.seqservice.netPathPrefixSearch.SUFFIX
The search prefix used to map the OutputRunFolder field in RunParameters.xml to the corresponding Linux directory. E.g., \nas\network\run_data
Default: \nas\network\run_data
No
integration.novaseq.seqservice.netPathPrefixReplace.SUFFIX
The directory where the sequencing service looks for run folders. E.g., /mnt/run_data
Default: /mnt/run_data
No
integration.novaseq.seqservice.netPathPrefixSearchReplaceSuffixes¹
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.
Property
Description
Configurable via System Setting
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))
Yes
integration.miseq.v8.seqservice.eventFileDirectory.1
A network location monitored for event files, e.g., /mnt/illumina/gls_events/
Default: /mnt/gls_events
No
integration.miseq.v8.seqservice.netPathPrefixSearch.1
The network directory prefix contained in the event file.
Default: \nas\network\run_data
No
integration.miseq.v8.seqservice.netPathPrefixReplace.1
The mapped network directory mount name on the server used to access the run data directory, e.g., /mnt/network/data
Default: /mnt/run_data
No
integration.miseq.v8.seqservice.eventFileDirectorySuffixes
A list of eventFileDirectory path entries to monitor for event files. The value is one or more comma-separated integers.
Default: 99
ℹ️ Configured on install to point to 1
No
integration.miseq.v8.seqservice.netPathPrefixSearchReplaceSuffixes
A list of netPathPrefix search and replace entries for transforming Windows to Linux network paths. The value is one or more comma-separated integers.
Default: 99
ℹ️ Configured on install to point to 1
No
integration.miseq.v8.seqservice.runReportViewsVersion
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.
Default: 0
No
integration.miseq.v8.seqservice.ignoreUnmatchedContainerIds
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
No
integration.miseq.v8.seqservice.ignoreUnmatchedContainerIdsWaitDays
The number of days between when the event is created and the event file is archived.
Default: 14
No
integration.miseq.v8.seqservice.synchronizationPeriod
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.
Property
Description
Configurable via System Setting
integration.miseqdx.seqservice.ignoreUnmatchedContainerIds
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’.
No
integration.miseqdx.seqservice.ignoreUnmatchedContainerIdsWaitDays
The number of days between when the event is created and the event file is archived.
Default: 14
No
integration.miseqdx.seqservice.synchronizationPeriod
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
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))
Yes
integration.miseqdx.seqservice.eventFileDirectory.1
A network location monitored for event files.
Default: /mnt/gls_events
No
integration.miseqdx.seqservice.netPathPrefixSearch.1
The network directory prefix contained in the event file.
Default: \nas\network\run_data
No
integration.miseqdx.seqservice.netPathPrefixReplace.1
The mapped network directory mount name on the server used to access the run data directory.
Default: /mnt/run_data
No
integration.miseqdx.seqservice.eventFileDirectorySuffixes
A list of eventFileDirectory path entries to monitor for event files. The value is one or more comma-separated integers.
Default: 99
No
integration.miseqdx.seqservice.runReportViewsVersion
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.
Default: 0
No
integration.miseqdx.seqservice.netPathPrefixSearchReplaceSuffixes
A list of netPathPrefix search and replace entries for transforming Windows to Linux network paths. The value is one or more comma-separated integers.
Default: 99
No
integration.miseqdx.seqservice.variantCallingProcessBaseName
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
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.
No
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)"
Yes
integration.sequencer_api.v2.novaseq.flowcells
List of supported NovaSeq flow cell types.
Type names exactly match the values used by the NVCS run status requests.
To add more types, provide both type and lanes properties, indented to the same point and starting with a dash (-).
Default: Flow cell type names. Example given below.
- type: "SP" lanes: 2
- type: "S1" lanes: 2
- type: "S2" lanes: 2
- type: "S4" lanes: 4
No
integration.sequencer_api.v2.novaseq.reagents
List of supported reagent kits to be tracked on sequencing steps.
lotName — The name of the lot as it appears in the run started request.
kitName — The name of the corresponding reagent kit in Clarity LIMS that the lot is tracked as.
To add more types, provide both type and lanes properties, indented to the same point and starting with a dash (-).
ℹ️ The name can differ in the NVCS request versus the Clarity LIMS configuration.
Default: Reagent kits to be tracked on sequencing step. Example given below.
- lotName: "Buffer" kitName: "Buffer Cartridge"
- lotName: "Cluster" kitName: "Cluster Cartridge"
- lotName: "SBS" kitName: "SBS Cartridge"
No
integration.sequencer_api.v2.novaseq.useReagentValidation
Configures whether or not to use reagent validation during retrieval of novaseq run recipe
Default: false
No
integration.sequencer_api.v2.novaseq.useSerialNumberForReagentLotNumber
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.
No
integration.sequencer_api.v2.recipe.sampleSheet.outputName integration.sequencer_api.v2recipe.sampleSheet.notAvailableValue
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.
Default: true
Yes
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).
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.
Property
Description
Configurable via System Setting
integration.sis.v2.maxNumberOfMessages
Maximum number of messages to return.
Valid values: 1 to 10
Refer to AWS Simple Queue Service API for details.
Default: 10
No
integration.sis.v2.receiveMessageWaitTimeSeconds
Time duration (in seconds) for which the call waits for a message to arrive in the queue before returning.
Refer to AWS Simple Queue Service API for details.
Default: 20
No
integration.sis.v2.maxMessageHandlingRetryTimes
The maximum number of times SIS core service will attempt to process the same message before discarding it.
Default: 3
No
integration.sis.v2.sqsPollingInterval
Time interval (in seconds) between each SQS message polling request. The interval should be greater than receiveMessageWaitTimeSeconds.
Default: 60
No
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