Last Updated: November 2024

Release Date: February 2024

Document Version: 2

These release notes describe the key changes to Illumina Preset Protocols (IPP) v2.7.

Compatibility

Refer to under Instruments & Integrations.

New Features

Added the NovaSeq X Series Sequencing v1.1 protocol, which does the following:

• Supports tracking the analysis status and high level analysis summary results at the meta workflow level.

• Supports the new 1.5B and 25B flow cell types. The B3 flow cell has been renamed to 10B.

• Updates the preset values of the final loading concentration in the Make Bulk Pool step.

Defects Fixed

None

Known Issues

None

Revision History

The Illumina Preset Protocols (IPP) v2.7 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 v2.7 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 configuration slices.

• Templates for the following uses:

  • Sample sheet generation

Protocols and Configuration Slices

IPP Integration v2.7 provides protocols that contain configuration slices. These configuration slices are used to install other workflows and protocols.

QC_Protocols

QC_Protocols configuration component contains the qc-protocols base slice. This configuration does not contain any workflows, but it does provide the following protocols that are used by 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 configuration slices and the workflows that are installed with IPP Integration v2.7.

AmpliSeq_for_Illumina_Protocols Configuration Slices and Workflows

Additional Configuration Slices

The following table shows additional configuration slices and workflows that are installed with IPP Integration v2.7.

Additional Configuration Slices and Workflows

IPP Integration v2.7 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:

If this is a new Clarity LIMS installation, you must install the QC_Protocols before the preconfigured workflows. The base configuration is included in the standard installation process.

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 v2.7 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:

Install Operation

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

For example, to install the qc-protocols slice, run the following command:

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 v2.7. To use the all operation at this level, run the following command:

• 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:

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 other selected slices.

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.

IPP Integration v2.7 Workflow Upgrades

There are some expected conflicts when upgrading from IPP Integration v2.6.

In IPP v2.7, new flow cell types are supported that cause a conflict with the NovaSeq X Flowcell Type derived sample custom field. The following workflows can be affected and lead to conflicts when upgrading from IPP v2.6 to v2.7:

• Illumina DNA Prep (M) Tagmentation v1.0.6

• Nextera Mate Pair v1.0.7

• Nextera XT DNA v2.0.7

• TruSeq DNA PCR-Free v2.0.7

To resolve these conflicts, perform the following actions:

1. 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.

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

   1. From Configuration, select the Custom Fields tab.