Illumina Instrument Sample Sheets

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.

Automation name

Enabled on master step/process type

Triggered by

Generate MiSeq SampleSheet

Denature and Dilute (MiSeq v1.0)¹

Manual button on Record Details screen

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.

ℹ️ The bcl2fastq2 sample sheet may be used with multiple instruments. The default configuration for the Illumina NextSeq integration is shown below.

Automation name

Configured on master step

Triggered by

Generate bcl2fastq2 NextSeq Samplesheet

Denature and Dilute (NextSeq 500/550 v1.0)¹

Manual button on Record Details screen

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.

Custom File Generation

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

Download the desired template. (See Attachments section below.)
Customize the template file as required. (See Template File Generator documentation.)
Upload the customized template file to the appropriate step automation.
A token for the template file is automatically added to the Tokens list.

In the automation command line, provide the file token as the -t (-templatePath) parameter value:

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