Last Updated: December 2024

Release Date: December 2024

These release notes describe the key changes to Illumina Preset Protocols (IPP) v2.10.

Compatibility

Refer to Compatibility under Instruments & Integrations.

New Features & Updates

• Added a new MiSeq i100 Series Sequencing v1.0 protocol that supports the new MiSeq i100 Series Integration Package v1.0.

• Added a new MiSeq i100 Series On-Prem Sequencing v1.0 protocol that supports the new MiSeq i100 Series On-Prem Integration Package v1.0.

• Added a new NovaSeq X Series On-Prem Sequencing v1.0 protocol that supports the new NovaSeq X Series On-Prem Integration Package v1.0.

• The updated NovaSeq X Series Sequencing v1.2 protocol supports NovaSeq X Series Integration Package v1.3.

• The updated NextSeq 500/550 Sequencing v1.3 protocol supports NextSeq 500/550 Integration Package v2.5.

• The updated Library Prep Validation v2.3.5 protocol now displays an expanded sample table under the Record Details milestone by default.

Known Issues

Importing workflows from IPP on Clarity v6.2 and v6.3 requires longer time (~8 times longer) compared to earlier versions (Clarity v6.1 and below). This issue is fixed in Clarity v6.3.1.

Additional References

Refer to these additional release notes for new features, updates and defects fixed for instrument integration protocols:

• MiSeq i100 Series On-Prem Integration v1.0.0 Release Notes

• MiSeq i100 Series Integration v1.0.0 Release Notes

• NextSeq 500/550 Integration v2.5.0 Release Notes

• NovaSeq X Series On-Prem Integration v1.0.0 Release Notes

• NovaSeq X Series Integration v1.3.0 Release Notes

This section describes the manual upgrade process from IPP v2.9 to IPP v2.10 to enable the changes described in Illumina Preset Protocols v2.10 Release Notes. If you do not want to upgrade the latest workflow through IPP, then update the workflow configuration manually using the following information.

The manual upgrade instructions include steps for:

1. Updating the sequencing instrument presets and routing scripts to support the new MiSeq i100 Series cloud, MiSeq i100 Series on-premise and NovaSeq X Series on-premise integrations.

2. Updating the precision of BP Aliquot Volume (ul) derived sample global field.

   ℹ BP Aliquot Volume (ul) field is used in Illumina Genomics Architecture - NovaSeq Sequencing v2.1, NovaSeq 6000 v3.8, NovaSeqDx v1.2 and NovaSeq X Series Sequencing v1.1 protocols in IPP v2.9.

3. Updating the Library Prep Validation v2.3.4 protocol:

   • to display an expanded sample table under the Record Details milestone by default.

   • to route libraries to new instruments. Refer to these steps for updating the routing scripts.

4. Updating the NovaSeq X Series Sequencing v1.1 protocol in IPP v2.9 to fix bugs. The steps involve updating container definition, step configuration, automations and global step fields. For manual upgrade instructions for the NovaSeq X Series Sequencing workflow, refer to NovaSeq X Series Integration v1.3.0 Manual Upgrade.

5. Updating the NextSeq 500/550 Sequencing v1.2 protocol in IPP v2.9 to support generation of forward-orientation samplesheet that is compatible with NextSeq 500/550 Control Software Version 4.2 and Local Run Manager (LRM) v4.0 for selected applications. For manual upgrade instructions for the NextSeq 500/550 Sequencing workflow, refer to NextSeq 500/550 Integration v2.5.0 Manual Upgrade.

1. Update Sequencing Instrument Presets

In IPP v2.10, new workflows are available. New options for the MiSeq i100 Series (cloud), MiSeq i100 Series (on-premise) and NovaSeq X Series (on-premise) integrations have been added.

This can cause a conflict with the Sequencing Instrument derived sample custom field. The following workflows can be affected:

• Illumina DNA Prep (M) Tagmentation v1.0.9

• Nextera Mate Pair v1.0.10

• Nextera XT DNA v2.0.10

• TruSeq DNA PCR-Free v2.0.10

• TruSeq Nano DNA v1.0.10

• Library Prep Validation v2.3.4

• TruSeq ChIP-Seq v1.0.10

• TruSeq Methyl Capture EPIC v2.0.11

• TruSeq Small RNA v1.0.10

• TruSeq Stranded mRNA v2.1.10

• TruSeq Custom Amplicon (TSCA) v1.0.10

• Nextera Rapid Capture Custom Enrichment v2.0.11

• TruSeq DNA Exome v2.0.10

• TruSeq RNA Access v2.0.10

• TruSight Tumor 170 v2.0.10

Force Import Workflows During Installation

When the expected conflicts are encountered during the IPP workflow installation, enter f to import the workflow when prompted. An example of the prompt is as follows.

Conflicts were detected between this workflow configuration package file and the existing configuration in the LIMS!
What would you like to do with this workflow configuration package file? [(f|Import anyway)|(s|Skip this workflow)|(a|Abort)]:

Add New Options to Sequencing Instrument Global Field

After the workflow is installed, resolve the conflicts as follows.

1. From Configuration, select the Custom Fields tab, and then select the Global Fields tab.

2. Search for Sequencing Instrument.

3. For Additional Options, add the following to the Dropdown Items list:

   • NovaSeq X Series On-Prem

   • MiSeq i100 Series

   • MiSeq i100 Series On-Prem

Update Routing Script Automations

Existing library preparation workflows may include routing scripts to integrations. These routing scripts have been updated to add new options for the MiSeq i100 Series (cloud), MiSeq i100 Series (on-premise) and NovaSeq X Series (on-premise) integrations. Modify the automation script as follows.

• [Optional] If you are using the MiSeq i100 Series (cloud) instrument, add the instrument to the script:

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  \
  --FIELD_NAME 'Sequencing Instrument' \
  --FIELD_VALUE 'MiSeq i100 Series' \
  --WORKFLOW 'MiSeq i100 Series Sequencing v1.0' \
  --STEP 'Assign Analysis Configuration Template (MiSeq i100 Series Sequencing v1.0)' \
  --INPUTS_OR_OUTPUTS 'OUTPUTS'

• [Optional] If you are using the MiSeq i100 Series (on-premise) instrument, add the instrument to the script:

  Copy

  \
  --FIELD_NAME 'Sequencing Instrument' \
  --FIELD_VALUE 'MiSeq i100 Series On-Prem' \
  --WORKFLOW 'MiSeq i100 Series On-Prem Sequencing v1.0' \
  --STEP 'Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v1.0)' \
  --INPUTS_OR_OUTPUTS 'OUTPUTS'

• [Optional] If you are using the NovaSeq X Series (on-premise) instrument, add the instrument to the script:

  Copy

  \
  --FIELD_NAME 'Sequencing Instrument' \
  --FIELD_VALUE 'NovaSeq X Series On-Prem' \
  --WORKFLOW 'NovaSeq X Series On-Prem Sequencing v1.0' \
  --STEP 'Assign Analysis Configuration Template (NovaSeq X Series On-Prem Sequencing v1.0)' \
  --INPUTS_OR_OUTPUTS 'OUTPUTS'

• [Optional] If you are using the NovaSeq X Series Sequencing workflow v1.2 for cloud, update the workflow version in the script:

  Copy

  --FIELD_NAME 'Sequencing Instrument' \
  --FIELD_VALUE 'NovaSeq X Series' \
  --WORKFLOW 'NovaSeq X Series Sequencing v1.2' \
  --STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.2)' \
  --INPUTS_OR_OUTPUTS 'OUTPUTS' \
  \

• [Optional] If you are using the NextSeq 500/550 Sequencing workflow v1.3, update the workflow version in the script:

  Copy

  --FIELD_NAME 'Sequencing Instrument' \
  --FIELD_VALUE 'NextSeq' \
  --WORKFLOW 'NextSeq 500/550 Sequencing v1.3' \
  --STEP 'Library Pooling (NextSeq 500/550 v1.3)' \
  --INPUTS_OR_OUTPUTS 'OUTPUTS' \
  \

2. Update BP Aliquot Volume (ul) Global (Derived Sample) Field

1. Select the Configuration tab, and then select the Custom Fields tab.

2. Under Global Fields, navigate to the Derived Sample section and update BP Aliquot Volume (ul):

   • Decimal Places Displayed from 0 to 1

3. Update Library Prep Validation to Display Expanded Sample Table by Default

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

2. Select Library Prep Validation workflow.

3. Select Library Prep Validation protocol.

4. Select Library Prep Validation step.

5. Select Record Details milestone.

6. Toggle Sample Display Default setting to Expand.

The Illumina Preset Protocols (IPP) v2.10 support the integration of Clarity LIMS with established lab protocols.

The integration provides preconfigured workflows that map to lab protocols and steps, and support Illumina library prep kits, reagent kits, assays, and instruments.

This guide provides instructions and describes the components installed in the default configuration of IPP.

Installation Components

IPP Integration v2.10 is distributed as the BaseSpaceLIMS-Illumina-Preset-Protocols RPM package. The RPM package installs the following components:

• The illumina-preset-protocols-installer.sh script for listing and importing available workflow configuration package files.

• Templates for the following uses:

  • Sample sheet generation

  • Sample placement pattern

  • Covid testing setup and reporting

  • Illumina Genomics Architecture (IGA)

• Automation scripts, including scripts to support IGA and Clarity LIMS Product Analytics (CLPA) automation.

• Workflow configuration package files.

Protocols and Configuration Package Files

IPP Integration v2.10 provides protocols that contain workflow configuration package files. These workflow configuration package files are used to install other workflows and protocols.

QC_Protocols

QC_Protocols configuration component contains the qc-protocols base configuration. This configuration does not contain any workflows, but it does provide the following protocols that can be incorporated into other workflows:

• DNA Initial QC

• Library Validation QC

• RNA Initial QC

The following table shows the components that are installed with the QC_Protocols configuration.

Components Installed with QC_Protocols

AmpliSeq_for_Illumina_Protocols

The following table shows the AmpliSeq_for_Illumina_Protocols workflow configuration package files and the workflows that are installed with IPP Integration v2.10.

AmpliSeq_for_Illumina_Protocols Configuration Package Files and Workflows

Additional Configuration Package Files

The following table shows additional workflow configuration package files and workflows that are installed with IPP Integration v2.10.

Additional Configuration Package Files and Workflows

IPP Integration Package Installation

The BaseSpaceLIMS-Ilumina-Preset-Protocols RPM package provides instructions for locating and running the /opt/gls/clarity/config/illumina-preset-protocols-installer.sh bash script that launches the IPP configuration installer.

The RPM package automatically installs template files that are used with Template File Generator (TFG) and Sample Placement Helper. These template files are accessible after the applicable configuration is installed. The files are installed at the following locations:

• /opt/gls/clarity/extensions/conf/driverfiletemplates

• /opt/gls/clarity/extensions/conf/infinium/placementpatterns

• /opt/gls/clarity/extensions/conf/covid

The RPM package automatically installs the CLPA automation that is used for the CLPA integration. This automation is installed at the following location:

/opt/gls/clarity/extensions/unified-product-analytics/automation

After you have selected a workflow, the installer validates the import of that workflow and provides Warning/Error details in STDOUT. This process allows you to proceed with the import or cancel it.

Installer Parameters and Operations

The IPP Integration v2.10 installer uses parameters and operations to assist with the configuration installation.

You must run the installer as the glsjboss user. The following table describes the parameters that are available for use with the installer.

IPP Installer Parameters

List Operation

Run the installer with the list operation for a list of all configuration installation options in a two-column format. The first column shows the IPP workflow identifier (or Id) that the installer uses when running the install operation. The second column shows the name of the configuration associated with the identifier. As the glsjboss user, run the following command to view the list of IPP workflows:

/opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o list

Install Operation

Use the install operation to install the workflow configuration package file. Specify both the name of the parent item and the name of the workflow configuration package file, separated by a period, as follows:

/opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o install Parent_Item_name.workflow_configuration_package_file_name

For example, to install the qc-protocols workflow configuration package file, run the following command:

/opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o install QC_Protocols.qc-protocols

All Operation

The all operation is a special option that is available at the top level and parent item level.

• At the top level, use the operation to install every configuration package from IPP Integration v2.10. To use the all operation at this level, run the following command:

  Copy

  bash /opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o install all

• At the parent item level, use the operation to install the workflows associated with a specific parent item. For example, run the following command to install the workflows associated with the AmpliSeq_for_Illumina_Protocols parent item:

  Copy

  bash /opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o install AmpliSeq_for_Illumina_Protocols.all

Headless Mode

Headless mode allows the install operation to complete without prompting for input. Use this mode if you want to automate the installation. When running the installation in headless mode, the process still runs through the validation phase before importing the configuration. However, if a conflict is found, the configuration causing the conflict is skipped automatically.

Installation Validation

The IPP installer validates the configuration import. If conflicts are found during the validation, a warning message displays. This message provides the following options:

• f/Import anyway

• s/Skip this workflow

• a/Abort

The f/Import anyway option runs the import command of the config slicer tool. It also allows the tool to handle conflicts. This option does not run the config slicer tool in importAndOverwrite mode.

The s/Skip this workflow option does not import workflows where conflicts were found, but continues to import the remaining workflow package files (if any).

The a/Abort option aborts all import operations. The conflicts found are captured in the log files and can be reviewed.

Track and Log the Installation

The IPP installer tracks the installation process in the installhistory table and generates log files that can be reviewed after the installation is complete.

java -jar /opt/gls/clarity/tools/propertytool/omxprops-ConfigTool.jar getInstallHistory

/opt/gls/clarity/logs/illumina-preset-protocols/{IPP version}/{Time-based Digits}/

/opt/gls/clarity/logs/illumina-preset-protocols/{IPP version}/{Time-based Digits}/