Step 4: Load to Library Tube Strip (NovaSeq X Series Sequencing v1.0)
The Load to Library Tube Strip (NovaSeq X Series Sequencing v1.0) step allows you to scan the library tube strip barcode into Clarity LIMS. Then, you can place the working pools into the library tube strip used in the NovaSeq X Series run. This step also does the following actions:
| • | Validates the run setup and analysis information. |
| • | Generates the sample sheet file. |
| • | Creates a planned run on ICA, depending on the selected run mode. |
The following automations are configured on this step:
| • | Validate Input Count and Validate Analysis Configurations and Register Step Started |
| • | Validate Library Tube Strip Barcode |
| • | Validate Run Setup and Create Planned Run |
| • | Set Next Step |
| • | Register Step Completed |
Validate Input Count and Validate Analysis Configurations and Register Step Started
Automatically triggered on entry to the step, this automation completes the following actions:
| • | Checks that the number of input pools is the same as the number of tubes in the library tube strip. |
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:validateSampleCount -min 8 -max 8
| • | Performs basic checks on the secondary analysis configuration of the samples in the same planned run. The following checks are included in this script: |
| – | Secondary analysis configuration of samples in a planned run is within maximum configuration limit. |
| – | Samples in a planned run have the same type of analysis (eg, Cloud or Local). |
| – | Samples in the same pools that have the same secondary analysis (eg, Illumina DRAGEN Enrichment) also have the same analysis settings (eg, Map/Align Output Format = CRAM) and the same analysis version (eg, v3.8.4). |
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/SIS/SISServices/extensions/automation/novaseqxseries-automation.jar script:validate_physical_logical_configurations -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -m PerRun script:validate_analysis_config -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -m PerRun && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:validate_same_analyte_udf_value_for_all_inputs -i {stepURI:v2} -u {username} -p {password} -l {compoundOutputFileLuid1} -f 'Run Mode' -perPool false
| • | Registers the start time of the step by publishing messages to CLPA through ICA. |
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/common/step_started.groovy'
Validate Library Tube Strip Barcode Automation
Automatically triggered on the Placement screen, this automation validates the library tube strip barcode to make sure that it conforms to the barcode mask LC[0-9]{7}-LC1.
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:validate_output_containers -l {compoundOutputFileLuid1} -r 'Library 8-tube Strip:LC[0-9]{7}-LC1' -max 1
Validate Run Setup and Create Planned Run Automation
Automatically triggered after a selection on the Record Details screen, this automation completes the following actions:
| • | Validates the parameters entered on the Record Details screen. These parameters are used to set up the run, generate the sample sheet file, and create the planned run in ICA, depending on the run mode. |
| – | Run Name can only contain alphanumeric, dash, underscore, or period characters. Do not use spaces. |
if (!step.::Run Name::.matches(::[a-zA-Z0-9-_]+[a-zA-Z0-9-_. ]*::)) { fail(::Run Name contains prohibited characters. Please check to make sure Run Name only contains alphanumeric characters, spaces, dashes and underscores. Run Name must start with alphanumeric, a dash or an underscore::); }
| – | Run Name cannot exceed 255 characters. |
if (step.::Run Name::.length() > 255) { fail(::Run Name shall not exceed 255 characters.::); };
| • | Checks the Index 1 Cycles and Index 2 Cycles field values. If Index 2 Cycles is greater than 0, the Index 1 Cycles value must be greater than 0 or an error can occur. |
if (step.::Index 2 Cycles:: > 0 && step.::Index 1 Cycles:: == 0) { fail(::Index 1 Cycles cannot be zero if Index 2 Cycles is non-zero::); };
| • | Generates the sample sheet. If you are in Cloud run mode, the automation creates the planned run in ICA. The sample sheet is attached to the step. |
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/SIS/SISServices/extensions/automation/novaseqxseries-automation.jar script:generate_sample_sheet -i {stepURI:v2} -u {username} -p {password} -c {compoundOutputFileLuid0} -l {compoundOutputFileLuid1}
There is a backend validation of the sample sheet content in ICA. This validation makes sure that the sample sheet is valid to set up a Local mode run and that it is ready for use with DRAGEN applications.
For more information on sample name character restrictions, refer to NovaSeq X Series Integration v1.1 Validation and Troubleshooting.
Set Next Step Automation
Automatically triggered on exit of the Record Details screen, this automation completes the following actions:
| • | Copies the Run Mode from input to output. |
| • | Sets the next step for samples to ADVANCE, advancing them to the AUTOMATED - Sequencing Run (NovaSeq X Series Sequencing v1.0) step. |
output.::Run Mode:: = input.::Run Mode::; nextStep = ::ADVANCE::
Register Step Completed Automation
Automatically triggered on exit of the step, this automation registers the completion time of the step by publishing messages to CLPA through ICA.
/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/unified-product-analytics/automation/unified-product-analytics-automation.jar script:executeUPAAutomationScript -i {stepURI:v2} -u {username} -p {password} -s 'com/illumina/upa/scripts/common/step_completed.groovy'
Master Step Fields
The following table shows the master step fields that are configured on the Load to Library Tube Strip (NovaSeq X Series Sequencing v1.0) step. These fields are required for sample sheet generation and planned run creation in ICA.
|
Field Name |
Field Type |
Options |
Additional Options and Dropdown Items |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Cloud Run ID |
Text |
Read Only |
Hidden Used for creating a planned run in ICA. Do not remove, rename, or modify this field as it can cause the integration to break.
|
|||||||||
|
Index 1 Cycles |
Numeric Dropdown |
Required Field Custom Entries |
Range = 0–20 Presets
|
|||||||||
|
Index 2 Cycles |
Numeric Dropdown |
Required Field Custom Entries |
Range = 0–20 Presets
|
|||||||||
|
Output Folder |
Text |
|
||||||||||
|
Read 1 Cycles |
Numeric Dropdown |
Required Field Custom Entries |
Range = 1–251 Presets
|
|||||||||
|
Read 2 Cycles |
Numeric Dropdown |
Required Field Custom Entries |
Range = 0–251 Presets
|
|||||||||
|
Run Mode |
Text Dropdown |
Required Field |
Presets
|
|||||||||
|
Run Name |
Text |
Required Field |
User Interaction
For more information, refer to the Load to Library Tube Strip (NovaSeq X Series Sequencing v1.0) step section in NovaSeq X Series Integration v1.1 Validation and Troubleshooting.
