It is possible to provide support for multiple, identical seqservice.netPathPrefixSearch property values. This is achieved by using the seqservice.eventFileDirsToUseForSearchReplacePair properties. These properties can be used to specify the mappings between search replace pairs and their associated event directories.

• The value of the seqservice.eventFileDirsToUseForSearchReplacePair property is a comma-separated list of event file directory suffixes to be applied to the search/replace pair.

• If the property is not supplied (or the value is left empty), the behavior is unchanged. In this case, the search/replace pair is treated as global and applied to all active event file directory suffixes.

By default, BaseSpace Clarity LIMS does not specify the eventFileDirsToUseForSearchReplacePair property. If you want the search/replace pair to apply only to a subset of the event file directories, you must supply the property manually.

The following example uses a MiSeq installation to show several configuration options, with comments. Similar configuration may be applied for installations of other Illumina instrument integrations (eg, MiSeqDx, NextSeq).

Note that the last part of this example shows configuration that results in an error.

miseq.v8.seqservice.eventFileDirectory.1 '/mnt/MiSeq1/data/gls_events'
miseq.v8.seqservice.eventFileDirectory.2 '/mnt/MiSeq2/data/gls_events'
miseq.v8.seqservice.eventFileDirectorySuffixes '1,2'

miseq.v8.seqservice.netPathPrefixSearch.1 'Y:\'
miseq.v8.seqservice.netPathPrefixReplace.1 '/mnt/Miseq1/data/'
miseq.v8.seqservice.eventFileDirsToUseForSearchReplacePair.1 '1' // just use search/replace pair 1 in dir 1
 
miseq.v8.seqservice.netPathPrefixSearch.2 'Y:\'
miseq.v8.seqservice.netPathPrefixReplace.2 '/mnt/Miseq2/data/'
miseq.v8.seqservice.eventFileDirsToUseForSearchReplacePair.2 '2' // just use search/replace pair 2 in dir 2
 
miseq.v8.seqservice.netPathPrefixSearch.3 'A:\'
miseq.v8.seqservice.netPathPrefixReplace.3 '/mnt/Miseq2/data/'
miseq.v8.seqservice.eventFileDirsToUseForSearchReplacePair.3 '1,2' // use search/replace pair 3 in dir 1 AND 2
 
miseq.v8.seqservice.netPathPrefixSearch.4 'B:\'
miseq.v8.seqservice.netPathPrefixReplace.4 '/mnt/Miseq2/data/'
miseq.v8.seqservice.eventFileDirsToUseForSearchReplacePair.4 '' // global, use this search/replace pair in all dirs
 
miseq.v8.seqservice.netPathPrefixSearch.5 'C:\'
miseq.v8.seqservice.netPathPrefixReplace.5 '/mnt/Miseq2/data/' // no replace pair dir prop specified = global, use this search/replace pair in all dirs
 
miseq.v8.seqservice.netPathPrefixSearch.6 'Y:\'
miseq.v8.seqservice.netPathPrefixReplace.6 '/mnt/Miseq2/data/'
miseq.v8.seqservice.eventFileDirsToUseForSearchReplacePair.6 '1' // duplicate search value (Y:) for event file dir 1 - ERROR
 
miseq.v8.seqservice.netPathPrefixSearchReplaceSuffixes '1,2,3,4,5,6'

Compatibility:

• Clarity LIMS v5.1 & later, with NGS Extensions v5.17 and later

Use the Template File Generator tool to generate custom sample sheets for upload to Illumina instruments.

The driver_file_generator script is invoked in an automation command line, typically configured on the step prior to the instrument run. By default, the automation is triggered by a button on the Record Details screen.

For details on the parameters used by the script, template file contents, and how to create custom template files, see the Template File Generator documentation.

MiSeq Control Software and bcl2fastq2-compatible sample sheet template files are available from the Clarity LIMS Support team.

MiSeq Sample Sheet Generation

This section summarizes the default configuration for MiSeq sample sheet generation. A template file that is compatible with MiSeq Control Software (MCS) is attached to this page.

¹ The version reflected in the master step may be different depending on the integration version you are using.

Automation command line:

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -i {processURI:v2} -u {username} -p {password} \
script:driver_file_generator \
-t /opt/gls/clarity/extensions/conf/driverfiletemplates/MiSeqSamplesheet.csv \
-o {compoundOutputFileLuid1}.csv \
-q true \
-destLIMSID {compoundOutputFileLuid1} \
-l {compoundOutputFileLuid2}"

For a description of the parameters used by the driver_file_generator script, see the Creating Template Files article.

In Clarity LIMS v5.1 and later, the automation is configured on the Automation configuration screen. By default, the automation is triggered by a manual button on the Record Details screen. The automation trigger settings are configured on the master step configuration screen.

bcl2fastq2 Sample Sheet Generation

This section summarizes the default configuration for bcl2fastq2 sample sheet generation.

Two bcl2fastq2 software-compatible template files are attached to this page. If you would like reverse complement sequences to be included in your sample sheet, use the BCL2FASTQ_Reverse_Complement_Samplesheet.csv template.

¹ The version reflected in the master step may be different depending on the integration version you are using.

Automation command line:

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -i {processURI:v2} -u {username} -p {password} \
script:driver_file_generator \
-t /opt/gls/clarity/extensions/conf/driverfiletemplates/{udf:Samplesheet Template} \
-o {compoundOutputFileLuid1}.csv \
-q true \
-destLIMSID {compoundOutputFileLuid1} \
-l {compoundOutputFileLuid2}"

or a description of the parameters used by the driver_file_generator script, see the Creating Template Files article.

In Clarity LIMS v5.1 and later, the automation is configured on the Automation configuration screen. By default, the automation is triggered by a manual button on the Record Details screen. The automation trigger settings are configured on the master step configuration screen.

Custom File Generation

To generate a custom sample sheet, complete the following steps:

1. Download the desired template. (See Attachments section below.)

2. Customize the template file as required. (See Template File Generator documentation.)

3. Upload the customized template file to the appropriate step automation.

   A token for the template file is automatically added to the Tokens list.
4. In the automation command line, provide the file token as the -t (-templatePath) parameter value:

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   bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -i {processURI:v2} -u {username} -p {password} \
   script:driver_file_generator \
   -t {file:myTemplate.csv} \
   -o {compoundOutputFileLuid1}.csv \
   -q true \
   -destLIMSID {compoundOutputFileLuid1} \
   -l {compoundOutputFileLuid2}"

   At run time, the token is replaced with the absolute path of the template file.

For instructions on uploading template files to an automation, and adding the token to the command line, see the following articles:

• Adding & Configuring Automations (Attaching template files to step automations document section) in the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

• Creating Template Files

Attachments

MiSeqSamplesheetv3.csv:

BCL2FASTQ_Samplesheet.csv:

BCL2FASTQ_Reverse_Complement_Samplesheet.csv:

Custom Field/User-Defined Field

As of Clarity LIMS v5.0.0, the term user-defined field (UDF) has been replaced with custom field in the user interface. However, the API resource is still called UDF.

There are two types of custom fields:

• Master step fields — Configured on master steps. Master step fields only apply to the following:

  • The master step on which the fields are configured.

  • The steps derived from those master steps.

• Global fields — Configured on entities (eg, submitted sample, derived sample, measurement, etc.). Global fields apply to the entire Clarity LIMS system.

Run Mode

The following run modes description currently applies for NextSeq 1000/2000 and NovaSeq X Series integrations

• Local run mode - Only the sample sheet is generated and stored on Clarity LIMS. Run/Analysis configuration is imported manually into the instrument via a sample sheet to start the run. The downstream secondary analysis is performed locally on the instrument using the onboard DRAGEN module.

• Hybrid/Cloud run mode - The planned run is created on ICA based on the run/analysis data from the integration service. The planned run contains all the run and analysis configuration required to start the run on the instrument. The sample sheet is also generated and stored on Clarity LIMS for reference purposes. In Cloud run mode, the analysis is performed on the cloud whereas in Hybrid run mode, the analysis is performed locally on the instrument using the onboard DRAGEN module.

To support planned run creation for samples having duplicate names with different indexes, updates are required on the library preparation workflow that these samples go through.

Follow these steps to update the output Naming Convention of the library preparation workflow.

1. Select the Configuration tab, and then select the Lab Work tab.

2. Under Master Steps, select the master step of the library preparation workflow (e.g., Library Prep Validation).

3. Navigate to the Step Type pane and update Naming Convention to

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   {SubmittedSampleName}_{OutputItemLIMSID}