Last Updated: November 2024

Release Date: June 2024

Document Version: 2

These release notes describe the key changes to Illumina Preset Protocols (IPP) v2.8.

Compatibility

Refer to Compatibility under Instruments & Integrations.

New Features

• Added a new NextSeq 1000/2000 On-Prem Sequencing v1.0 protocol that supports the NextSeq 1000/2000 On-Prem Integration Package v1.0.

• Updated the NextSeq 1000/2000 Sequencing v2.4 protocol to support NextSeq 1000/2000 Integration Package v2.5.

• Updated the following protocols to support the new Illumina DNA/RNA UD Indexes Sets A–D:

  • Illumina COVIDSeq Workflow

  • Illumina DNA PCR-Free Library Prep Manual

  • Illumina DNA Prep (M) Tagmentation

  • Illumina Stranded mRNA Prep Ligation

  • Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus

  • Illumina DNA Prep with Enrichment (S) Tagmentation

  • Illumina RNA Prep with Enrichment (L) Tagmentation

• Updated the sequencing instrument presets and routing scripts to remove the HiSeq series of instruments.

• Updated the step output naming convention for the Library Prep Validation protocol.

Defects Fixed

• Removed Sample_Well field from MiSeq-generated sample sheet for sample sheet to be compatible with the MiSeq RUO Local Run Manager v4.1.

Known Issues

• There is an import issue when you try to import TruSeq RNA Exome v1.05 from IPP v2.8 after it has been imported to Clarity LIMS from IPP v2.7. This issue is due to a missed protocol version upgrade for the TruSeq RNA Exome in IPP v2.8.

• Due to a known with the config slicer tool, importing workflows and protocols from IPP on Clarity v6.2 and v6.3 requires longer time (~ 8 times) compared to earlier versions (Clarity v6.1 and below).

Revision History

This section describes the manual upgrade process from IPP v2.7 to IPP v2.8 to enable the changes described in Illumina Preset Protocols v2.8 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 for IPP v2.8 include the following information:

• Support for the new Illumina DNA/RNA UD Indexes Sets A–D.

• A sample sheet bug fix for the MiSeq v3.2 workflow.

• Updates to the sequencing instrument presets and routing scripts to remove the HiSeq series instruments and to support the new NextSeq 1000/2000 on-premise integration. For manual upgrade instructions for the NextSeq 1000/2000 Sequencing workflow, refer to NextSeq 1000/2000 Integration v2.5.0 Manual Upgrade.

• An update to the step output naming convention for Library Prep Validation.

  This modification supports generation of planned run using samples having duplicate names with different indexes for NextSeq 1000/2000 and NovaSeq X Series sequencers.

DNA/RNA UD Indexes

To support the new DNA/RNA UD indexes, you must upload the new label list files and add the label groups to steps within the protocols.

Upload Label List Files

Download the following label list files and upload them to Clarity LIMS as new label groups. For instructions, refer to Add and Configure Labels and Label Groups in the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

Illumina DNA-RNA UD Indexes Set A B C D Tagmentation (MD5 = 99d5c7159677638ad1c67dfd07c7b675):

Illumina DNA-RNA UD Indexes Set A Tagmentation (MD5 = 39952f3e644ab0889cb5a17ece76eb37):

Illumina DNA-RNA UD Indexes Set B Tagmentation (MD5 = d1ab38606a6af2837bf70a20faaad39a):

Illumina DNA-RNA UD Indexes Set C Tagmentation (MD5 = c562e964d1958cdf7900e2d50805a2a9):

Illumina DNA-RNA UD Indexes Set D Tagmentation (MD5 = 8dc20541d231c226784c43791ec7c6fb):

Illumina RNA UD Indexes Set A B C D Ligation (MD5 = f79e72899e02b546fc93b977546e83ae):

Illumina RNA UD Indexes Set A Ligation (MD5 = 733f11e1462989d1f5a7c1e933214f71):

Illumina RNA UD Indexes Set B Ligation (MD5 = 0fda17945b89a12f0093bc01b5492519):

Illumina RNA UD Indexes Set C Ligation (MD5 = dd3dffc584d11987224bc7c968d2939b):

Illumina RNA UD Indexes Set D Ligation (MD5 = 47a067849c9b20eebe100e96156a4fdd):

Add Label Groups to Steps in Protocols

From the Add Labels tab of the Configuration page, add the following label groups for each protocol or master step in the table for workflows when upgrading from IPP v2.7 to IPP v2.8:

• Illumina DNA-RNA UD Indexes Set A B C D Tagmentation

• Illumina DNA-RNA UD Indexes Set A Tagmentation

• Illumina DNA-RNA UD Indexes Set B Tagmentation

• Illumina DNA-RNA UD Indexes Set C Tagmentation

• Illumina DNA-RNA UD Indexes Set D Tagmentation

From the Add Labels tab of the Configuration page, add the following label groups for each protocol or master step in the table:

• Illumina RNA UD Indexes Set A B C D Ligation

• Illumina RNA UD Indexes Set A Ligation

• Illumina RNA UD Indexes Set B Ligation

• Illumina RNA UD Indexes Set C Ligation

• Illumina RNA UD Indexes Set D Ligation

MiSeq v3.2 Sample Sheet Bug Fix

Replace the MiSeqSamplesheetv3.csv file at

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

Update Sequencing Instrument Presets

The following are obsolete and removed as options for the Sequencing Instrument derived sample custom field:

• HiSeq2500

• HiSeq3000/4000

• HiSeqX

A new option for the NextSeq 1000/2000 on-premise integration has been added. The preset options have been reordered as follows.

• MiSeq

• NextSeq

• NextSeq 1000/2000

• NextSeq 1000/2000 On-Prem

• NovaSeq 2.0

• NovaSeq 3.0

• NovaSeqDx

• NovaSeq X Series

Update Routing Scripts

The routing script needs to be updated to remove the routing options for obsolete instruments and to add a new option for the on-premise integration of the NextSeq 1000/2000. Modify the automation script as follows.

1. Remove the HiSeq instruments from the script:

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   --FIELD_NAME 'Sequencing Instrument' \
   --FIELD_VALUE 'HiSeq2500' \
   --WORKFLOW 'HiSeq 2500 Sequencing v1.0' \
   --STEP 'Library Pooling (HiSeq 2500 v1.0)' \
   --INPUTS_OR_OUTPUTS 'OUTPUTS' \
   \
   --FIELD_NAME 'Sequencing Instrument' \
   --FIELD_VALUE 'HiSeq3000/4000' \
   --WORKFLOW 'HiSeq 3000/4000 Sequencing v1.0' \
   --STEP 'Library Pooling (HiSeq 3000/4000 v1.0)' \
   --INPUTS_OR_OUTPUTS 'OUTPUTS' \
   \
   --FIELD_NAME 'Sequencing Instrument' \
   --FIELD_VALUE 'HiSeqX' \
   --WORKFLOW 'HiSeq X Sequencing v1.0' \
   --STEP 'Library Pooling (HiSeq X v1.0)' \
   --INPUTS_OR_OUTPUTS 'OUTPUTS' \
   \

2. Add the on-premise NextSeq 1000/2000 instrument to the script:

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   \
   --FIELD_NAME 'Sequencing Instrument' \
   --FIELD_VALUE 'NextSeq 1000/2000 On-Prem' \
   --WORKFLOW 'NextSeq 1000/2000 On-Prem Sequencing v1.0' \
   --STEP 'Library Pooling and Dilution (NextSeq 1000/2000 On-Prem Sequencing v1.0)' \
   --INPUTS_OR_OUTPUTS 'OUTPUTS'"

3. [Optional] If you are using the NextSeq 1000/2000 Sequencing workflow v2.4, update the workflow version in the script:

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   --FIELD_NAME 'Sequencing Instrument' \
   --FIELD_VALUE 'NextSeq 1000/2000' \
   --WORKFLOW 'NextSeq 1000/2000 Sequencing v2.4' \
   --STEP 'Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4)' \
   --INPUTS_OR_OUTPUTS 'OUTPUTS' \
   \

Update Library Prep Validation Step Output Naming Convention

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

2. Under Master Steps, select the Library Prep Validation master step.

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

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   {SubmittedSampleName}_{OutputItemLIMSID}

The Illumina Preset Protocols (IPP) v2.8 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 v2.8 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

  • 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.

• Configuration slices.

• Workflows for applicable instrument integrations.

Protocols and Configuration Slices

IPP Integration v2.8 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 v2.8.

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 v2.8.

Additional Configuration Slices and Workflows

IPP Integration v2.8 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

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 v2.8 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 configuration slices. Specify both the name of the parent item and the name of the configuration slice, separated by a period, as follows:

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

For example, to install the qc-protocols slice, 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 v2.8. To use the all operation at this level, run the following command:

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  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:

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  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 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.

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}/

IPP Integration v2.8 Workflow Upgrades

There are some expected conflicts when upgrading from IPP Integration v2.7.

In IPP v2.8, the on-premise NextSeq 1000/2000 is now supported and can cause a conflict with the Sequencing Instrument derived sample custom field. The following workflows can be affected:

• Illumina DNA Prep (M) Tagmentation v1.0.7

• Nextera Mate Pair v1.0.8

• Nextera XT DNA v2.0.8

• TruSeq DNA PCR-Free v2.0.8

• TruSeq Nano DNA v1.0.8

• Library Prep Validation v2.3.2

• TruSeq ChIP-Seq v1.0.8

• TruSeq Methyl Capture EPIC v2.0.9

• TruSeq Small RNA v1.0.8

• TruSeq Stranded mRNA v2.1.8

• TruSeq Custom Amplicon (TSCA) v1.0.8

• Nextera Rapid Capture Custom Enrichment v2.0.9

• TruSeq DNA Exome v2.0.8

• TruSeq RNA Exome v1.0.5

• TruSeq RNA Access v2.0.8

• TruSight Tumor 170 v2.0.8

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.

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

2. 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 NextSeq 1000/2000 On-Prem to the Dropdown Items list.