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IPP v2.6

Installation and User Configuration

The Illumina Preset Protocols (IPP) v2.6 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 v2.6 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.

Sample Sheet Generation Templates

BCL2FASTQ_Reverse_Complement_Samplesheet.csv
BCL2FASTQ_Samplesheet.csv
genomeStudio_Genotyping_SampleSheet_driver_file.csv
genomeStudio_Methylation_SampleSheet_driver_file.csv
iSeq_Samplesheet.csv
iSeqManual_Samplesheet.csv
miniSeq_Samplesheet.csv
MiSeqSamplesheetv3.csv
NextSeq1K2K_Pool1.csv
NextSeq1K2K_Pool2.csv
NextSeq1K2K_Pool3.csv
NovaSeq_BCL2FASTQ_Samplesheet.csv
NovaSeq_BCL2FASTQ_Samplesheet_v2.csv
NovaSeq_BCL2FASTQ_Reverse_Complement_Samplesheet.csv
NovaSeq_Standard_Bulk_Pool1.csv
NovaSeq_Standard_Bulk_Pool2.csv
NovaSeq_Standard_Bulk_Pool3.csv
NovaSeq_Xp_Bulk_Pool.csv
NovaSeq_Xp_Bulk_Pool2.csv
NovaSeq_Xp_Working_Pool.csv
NovaSeq_Xp_Working_Pool2.csv
NovaSeqDx_BCL2FASTQ_Samplesheet.csv
NovaSeqXSeries_Bulk_Pool1.csv
NovaSeqXSeries_Bulk_Pool2.csv
NovaSeqXSeries_Dilute_Denature_Calculate_Volumes.csv

Sample Placement Pattern Templates

Hybrid Pattern_96 well plate_8x1 HD BeadChip.tsv
Hybrid Pattern_96 well plate_8x1 LCG BeadChip.tsv
Hybrid Pattern_96 well plate_12x1 HD BeadChip.tsv
Hybrid Pattern_96 well plate_24x1 HD BeadChip.tsv
Hybrid Pattern_96 well plate_24x1 HTS BeadChip.tsv
Hybrid Pattern_96 well plate_24x1 HTS BeadChip Multichannel.tsv
Hybrid Pattern_96 well plate_24x4 XT BeadChip.tsv

Illumina Genomics Architecture (IGA) Templates

BatchingInputFile_template.csv
CaptureWashInputFile_template.csv
ExtractionInputFile_template.csv
LibInputFile_NFE_template_withoffsets.csv
LibInputFile_NFPF_template_withoffsets.csv
LoadToFlowcell_NovaSeqXp_Incomplete_template.csv
LoadToFlowcell_NovaSeqXp_ManifestForConsolidation_template.csv
LoadToFlowcell_NovaSeqXp_template.csv
LoadToLibTubeFile_NovaSeqStd_template.csv
MakeBPFile_NovaSeq_template.csv
PlatingInputFile_template.csv

Python Scripts for Automation Support

autoPlaceCovid7500.py
clarityapiutil.py
parseCovidSeqRunReport.py
verifyBeadChipIDs.py

Python Scripts for IGA Automation Support

glsapiutil:
- glsapiutil.py
- glsapiutil3.py
hamilton_fast_prep:
- 01_A_CFP_Batching_defaultContainerCheck.py
- 01_CFP_Batching_confirmPlateID.py
- 01_CFP_Batching_confirmPlateIDAndStoreInstrumentID.py
- 02_ReagentParsing.py
- 03_checkHamiltonFileNameBarcode.py
- 04_A_checkIndexPlateBarcodeWithCategory.py
- 04_B_autoAssignIndexesFromIndexPlanning.py
- 05_reusedIndexPlateWarning.py
- countSamples.py
- countSamplesInPools.py
- validate_sample_placement.py
iga_helpers:
- clarityUIFileHelper.py
- pop_up_msg.py
- printCurrentWorkflow.py
iga_novaseq:
- 01_NovaSeqStd_confirmPlateIDAndStoreInstrumentID_OptionalFile.py
- 02_NovaSeqStd_confirmPlateIDAndStoreInstrumentID_OptionalFile_DiluteDenature.py
- 03_NovaSeqXp_confirmBPPPlateAndStoreInstrumentID.py
- 03_NovaSeqXp_consolidateBulkPoolFiles.py
- 04_NovaSeqXp_completeAndConsolidateWPPZipFile.py
- NovaSeq_automated_warning.py
- NovaSeq_pooling_warning.py
- validate_floorcell_container.py
- validate_flowcell_pools.py
- validate_multiple_destination_plates.py
illumina-cobalt-samplesheet-converter:
- ss_converter
- converter.py
- errors.py
- v1_builder_plugins.py
- v1_v2_handler.py
- v2_converter_plugins.py
index_correct
- apply_correction_factors.py
make_bpp:
- apply_multiple_bulk_pools.py
- calculate_sample_volume.py
utils:
- common.py
- igaapiutil.py

Clarity LIMS Product Analytics Automation Script

unified-product-analytics-automation.jar

Configuration Slices

The following configuration slices are included in IPP Integration v2.6:

Illumina_Instruments, including:
- iScan-v1.0
- iSeq-100-v1.0
- Library-Prep-Validation-v2.3
- miniSeq-v1.0
- miseq-v3.2
- NextSeq1k2k-v2.3
- nextseq550-v1.1
- novaseq-v3.8
- novaseqdx-v1.2
- NovaSeqXSeries-v1.0
QC_Protocols
- qc-protocols
Ampliseq_for_Illumina_Protocols, including:
- AmpliSeq-Illumina-BRCA-Panel-v1.1
- AmpliSeq-Illumina-Cancer-HotSpot-Panel-V2-v1.1
- AmpliSeq-Illumina-Childhood-Cancer-Panel-v1.1
- AmpliSeq-Illumina-Comprehensive-Cancer-Panel-v1.1
- AmpliSeq-Illumina-Comprehensive-Panel-v3-v1.1
- AmpliSeq-Illumina-Custom-DNA-Panel-v1.1
- AmpliSeq-Illumina-Focus-Panel-v1.1
- AmpliSeq-Illumina-Immune-Repertoire-Panel-v1.1
- AmpliSeq-Illumina-Immune-Response-Panel-v1.1
- AmpliSeq-Illumina-Myeloid-Panel-v1.1
- AmpliSeq-Illumina-TCR-beta-SR-Panel-v1.1
- AmpliSeq-Illumina-Transcriptome-Human-Gene-Expression-Panel-v1.1
Covid, including:
- CDC-COVID-19-RT-PCR-v1.1
- Illumina-COVIDSeq-Workflow-v1.5
- Respiratory-Virus-Panel-v1.0
DNA_Protocols, including:
- ILASS-TruSight-Whole-Genome-Assay-v1.2
- Illumina-DNA-PCR-Free-Library-Prep-Manual-v1.0
- Illumina-DNA-Prep-M-Tagmentation-v1.0
- Nextera-Mate-Pair-v1.0
- Nextera-XT-v2.0
- TruSeq-DNA-PCR-Free-v2.0
- TruSeq-Nano-DNA-v1.0
IGA, including:
- IGA_Library_Prep_Automated_v2.1
- IGA_NovaSeq_Sequencing_v2.2
Infinium_Array, including:
- Genome-Studio-v1.0
- ILASS-Infinium-Genotyping-Assay-v1.0
- Infinium-HD-Methylation-Assay-Manual-v1.2
- Infinium-HTS-Assay-Manual-v1.2
- Infinium-LCG-Assay-Manual-v1.2
- Infinium-XT-Assay-Manual-v1.2
Methylation_Protocols, including:
- TruSeq-ChIP-Seq-v1.0
- TruSeq-Methyl-Capture-EPIC-v2.0
RNA_Protocols, including:
- Illumina-Stranded-mRNA-Prep-Ligation-v1.0
- Illumina-Stranded-Total-RNA-Prep-Ligation-with-Ribo-Zero-Plus-v1.0
- TruSeq-Small-RNA-v1.0
- TruSeq-Stranded-mRNA-v2.1
Targeted_Amplicon_Protocols
- TruSeq-Custom-Amplicon-v1.0
Targeted_Enrichment_Protocols, including:
- Illumina-DNA-Prep-with-Enrichment-S-Tagmentation-v1.1
- Illumina-RNA-Prep-with-Enrichment-L-Tagmentation-v1.0
- Nextera-Rapid-Capture-Custom-Enrichment-v2.0
- TruSeq-DNA-Exome-v2.0
- TruSeq-RNA-Exome-v1.0
TruSight_Oncology_Protocols, including:
- TruSight-Oncology-500-ctDNA-v1.1
- TruSight-Oncology-500-HT-v1.1
- TruSight-Oncology-500-v1.1
- TruSight-Tumor-170-v2.0

Instruments and Workflows

IPP Integration v2.6 contains workflows that are used to integrate the following instruments:

iScan
iSeq
MiSeq
MiniSeq
NextSeq 500/550
NextSeq 1000/2000
NovaSeq 6000
NovaSeq 6000Dx
NovaSeq X Series

The following workflows are included in the integration:

iScan v1.0
iSeq 100 v1.0
Library Prep Validation v2.3.1 (includes the applicable library prep workflows for each integration)
MiniSeq v1.0
MiSeq Sequencing v3.2
NextSeq 500/550 Sequencing v1.1
NovaSeq 6000 v3.8
NextSeq 1000/2000 Sequencing v2.3
NovaSeqDx v1.2
NovaSeq X Series Sequencing v1.0

These workflows require ClarityLIMS-NGS-Package v5.23.0 or later so that the Template File Generator tool can be used.

Protocols and Configuration Slices

IPP Integration v2.6 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 v2.6.

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 v2.6.

Additional Configuration Slices and Workflows

IPP Integration v2.6 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.

Prerequisites

Before installing the RPM package, make sure that the following software is installed:

Clarity LIMS v6.2 or later
NGS-Package v5.23.0 or later
SecretUtil v1.2. For more information, refer to Guide to Secret Management in the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

RPM Installation

On the server used for the IPP RPM installation, log in as the root user.
Use the yum command to install the RPM. The command line is as follows.
The --enablerepo piece of the command line must be included to enable the repo. The Illumina Support team provides the repo file and the appropriate name to use.
```
yum install BaseSpaceLIMS-Illumina-Preset-Protocols --enablerepo=<< repo name info from support >>
```
When you are prompted to proceed with the RPM package installation, enter y to confirm.

For information on running the installer and supported commands, parameters, and options, refer to Installer Parameters and Operations.

Installer Parameters and Operations

The IPP Integration v2.6 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 v2.6. To use the all operation at this level, run the following command:
```
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:
```
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.

Viewing the installhistory Table

After installation is complete, a record is stored in the installhistory table in the database.

To view the installation record, use the following command:

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

If a configuration slice is installed multiple times, there are multiple entries in the record. This scenario can happen during an upgrade or if there are attempts to resolve conflicts during installation. The log shows the following information for each slice:

Product — The name of the slice (e.g., IPP - LIMS 5 - TruSight_Oncology_Protocols.TruSight-Oncology-500-HT-v1.0).
Version — The version of the configuration slice that was installed (e.g., 2.0.0.25).
InstallDate — The time stamp for when the slice was installed. The date displays first (in YYYY-MM-DD format), followed by the time (in HH:MM:SS format)

Viewing the Log Files

After the configuration package is installed, the following log files are available:

ipp-installer.log
configslicer.log
omxprops.log

The ipp-installer.log file captures the output of the IPP installer tool. The name and location of this file can be changed with the command line options described previously. The default location is as follows:

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

The configslicer.log and omxprops.log files are raw outputs from their respective tools. These files contain more detail than the ipp-installer.log file. For example, if a conflict is identified in the ipp-installer.log file, the configslicer.log file shows the specific entry causing the conflict. Some workflow selections, such as the MiSeq and NextSeq integration workflows, import database properties in addition to a configuration slice.

By default, only the ipp-installer.log file is generated in the following directory:

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

When the -l operation is specified during installation, all three log files are available in the current working directory.

Manual Upgrade

Illumina Preset Protocols (IPP) v2.6 includes changes to some workflows.

This section describes the manual upgrade process from IPP v2.5 to IPP v2.6. If you do not want to upgrade the latest workflow through IPP, then update the workflow configuration manually using the following information.

In Clarity LIMS v6.2, symbolic links for Python 2 and Python 3 have been removed. For existing users upgrading from Clarity LIMS v5.x and v6.x to Clarity LIMS v6.2, Python scripts have to explicitly call Python2 and Python3.

IPP v2.6 supports the following workflows:

MiSeq Sequencing v3.2
- Includes validation to ensure single input in the Denature and Dilute step
NovaSeq 6000 v3.8
- Includes CLPA-enabled automations and scripts in the workflow
Illumina COVIDSeq Workflow v1.5
- Updates the Validate Flowcell Barcode automation in the Load to Flowcell Step of NovaSeq Xp Protocol to support the future flowcell barcode format
- Updates automation scripts to use Python 3 instead of Python 2
CDC Covid 19 RT PCR Workflows
- Includes the PCR Product LIMSID global field
- Updates automation scripts to use Python 3 instead of Python 2
Infinium HD Methylation Assay Manual v1.2
- Updates automation scripts to use Python 3 instead of Python 2
Infinium HTS Assay Manual v1.2
- Updates automation scripts to use Python 3 instead of Python 2
Infinium LCG Assay Manual v1.2
- Updates automation scripts to use Python 3 instead of Python 2
Infinium XT Assay Manual v1.2
- Updates automation scripts to use Python 3 instead of Python 2

IPP v2.6 also includes the following workflow changes that do not impact functionality:

Routing Automation script update for the various Library Preparation workflows with the following updated workflow versions:
- Illumina DNA Prep (M) Tagmentation v1.0.6
- Library Prep Validation v2.3
- Nextera Mate Pair v1.0.7
- Nextera Rapid Capture Custom Enrichment v2.0.8
- Nextera Rapid Capture Custom Enrichment v2.0.8
- TruSeq ChIP-Seq v1.0.7
- TruSeq Custom Amplicon (TSCA) v1.0.7
- TruSeq DNA Exome v2.0.7
- TruSeq DNA PCR-Free v2.0.7
- TruSeq Methyl Capture EPIC v2.0.8
- TruSeq Nano DNA v1.0.7
- TruSeq RNA Access v2.0.7
- TruSeq Small RNA v1.0.7
- TruSeq Stranded mRNA v2.1.7
- TruSight Tumor 170 v2.0.7
Workflow and step renaming to standardize the naming format within workflows for the following:
- NextSeq 500/550 Sequencing v1.1
- NovaSeqDx v1.2
- AmpliSeq Illumina BRCA Panel
  - Equalizer Workflow AmpliSeq for Illumina BRCA Panel v1.1
  - Library Prep AmpliSeq for Illumina BRCA Panel v1.1
  - Standard Workflow AmpliSeq for Illumina BRCA Panel v1.1
- AmpliSeq Illumina Cancer HotSpot Panel V2
  - Library Prep AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1
  - Standard Workflow AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1
- AmpliSeq Illumina Childhood Cancer Panel
  - DNA Library Prep AmpliSeq for Illumina Childhood Cancer Panel v1.1
  - Equalizer Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1
  - RNA Library Prep AmpliSeq for Illumina Childhood Cancer Panel v1.1
  - Standard Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1
- AmpliSeq Illumina Comprehensive Cancer Panel
  - Equalizer Workflow AmpliSeq for Illumina Comprehensive Cancer Panel v1.1
  - Library Prep AmpliSeq for Illumina Comprehensive Cancer Panel v1.1
  - Standard Workflow AmpliSeq for Illumina Comprehensive Cancer Panel v1.1
- AmpliSeq Illumina Comprehensive Panel v3
  - DNA Library Prep AmpliSeq for Illumina Comprehensive Panel v3 v1.1
  - Equalizer Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1
  - RNA Library Prep AmpliSeq for Illumina Comprehensive Panel v3 v1.1
  - Standard Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1
- AmpliSeq Illumina Custom DNA Panel
  - Equalizer Workflow AmpliSeq for Illumina Custom DNA Panel v1.1
  - Library Prep AmpliSeq for Illumina Custom DNA Panel v1.1
  - Standard Workflow AmpliSeq for Illumina Custom DNA Panel v1.1
- AmpliSeq Illumina Focus Panel
  - DNA Library Prep AmpliSeq for Illumina Focus Panel v1.1
  - Equalizer Workflow AmpliSeq for Illumina Focus Panel v1.1
  - RNA Library Prep AmpliSeq for Illumina Focus Panel v1.1
  - Standard Workflow AmpliSeq for Illumina Focus Panel v1.1
- AmpliSeq Illumina Immune Repertoire Panel
  - Equalizer Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.1
  - RNA Library Prep AmpliSeq for Illumina Immune Repertoire Panel v1.1
  - Standard Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.1
- AmpliSeq Illumina Immune Response Panel
  - Equalizer Workflow AmpliSeq for Illumina Immune Response Panel v1.1
  - RNA Library Prep AmpliSeq for Illumina Immune Response Panel v1.1
  - Standard Workflow AmpliSeq for Illumina Immune Response Panel v1.1
- AmpliSeq Illumina Myeloid Panel
  - DNA Library Prep AmpliSeq for Illumina Myeloid Panel v1.1
  - Equalizer Workflow AmpliSeq for Illumina Myeloid Panel v1.1
  - RNA Library Prep AmpliSeq for Illumina Myeloid Panel v1.1
  - Standard Workflow AmpliSeq for Illumina Myeloid Panel v1.1
- AmpliSeq Illumina TCR beta-SR Panel
  - DNA Library Prep AmpliSeq for Illumina TCR beta-SR Panel v1.1
  - RNA Library Prep AmpliSeq for Illumina TCR beta-SR Panel v1.1
- AmpliSeq Illumina Transcriptome Human Gene Expression Panel
  - Equalizer Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1
  - RNA Library Prep AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1
  - Standard Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1

Update MiSeq and NovaSeq 6000 v3 Workflows

For the MiSeq workflow, refer to MiSeq Integration v8.2 Manual Upgrade. For the NovaSeq 6000 workflow, refer to NovaSeq 6000 Integration v3.6.0 Manual Upgrade.

Update Automations for Illumina COVIDSeq Workflow v1.4 Workflow

From Configuration, select the Automation tab.
Under the Step Automation tab, search for the Validate Flowcell Barcode automation.
Update the existing command line as follows.
Changes to the existing command line are in red.
bash -l -c "/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:evaluateDynamicExpression \ -exp 'if ((input.::Flowcell Type:: == ::SP:: && !output.container.name.matches(::[A-Z0-9]{5}DR[A-Z0-9]{2}::)) { fail(::Invalid Flowcell Barcode. Please verify and try again.::) }; if (input.::Flowcell Type:: == ::S1:: && !output.container.name.matches(::[A-Z0-9]{5}DR[A-Z0-9]{2}::))) { fail(::Invalid Flowcell Barcode. Please verify and try again.::) }; if (input.::Flowcell Type:: == ::S2:: && !output.container.name.matches(::[A-Z0-9]{5}DM[A-Z0-9]{2}::))) { fail(::Invalid Flowcell Barcode. Please verify and try again.::) }; if (input.::Flowcell Type:: == ::S4:: && !output.container.name.matches(::[A-Z0-9]{5}DS[A-Z0-9]{2}::))) { fail(::Invalid Flowcell Barcode. Please verify and try again.::) }; output.::Flowcell Type:: = input.::Flowcell Type::; output.::Loading Workflow Type:: = input.::Loading Workflow Type::'\ -log {compoundOutputFileLuid1}"
Select Save.
From Configuration, select the Automation tab.
Under the Step Automation tab, search for the CovidSEQ: Parse TSV Run Report automation.
Update the existing command line from python to python3 as follows.
Changes to the existing command line are in red.
/usr/bin/python3/opt/gls/clarity/extensions/conf/covid/parseCovidSeqRunReport.py -u {username} -p {password} -s {stepURI} -f {compoundOutputFileLuid1} -g {compoundOutputFileLuid3}
Select Save.

Update CDC Covid 19 RT PCR Workflows

Create the PCR Product LIMSID global field as follows.
1. From Configuration, select the Custom Fields tab.
2. Under the Global Fields tab, create a new Submitted Sample field with the following attributes:
  - Name: PCR Product LIMSID
  - Field Type: Text
  - Required Field: No
  - Read Only: No
Update the automation as follows.
1. From Configuration, select the Automation tab.
2. Under the Step Automation tab, search for the auto placement for 7500 Covid-19 assay automation.
3. Update the existing command line from python to python3 as follows.
  Changes to the existing command line are in red.
  /usr/bin/python3/opt/gls/clarity/extensions/conf/covid/autoPlaceCovid7500.py -u {username} -p {password} -s {stepURI}
Select Save.

Update Infinium Assay Manual Workflows

This update applies to the following workflows:

Infinium HD Methylation Assay Manual v1.2
Infinium HTS Assay Manual v1.2
Infinium LCG Assay Manual v1.2
Infinium XT Assay Manual v1.2

Update the workflows as follows.

From Configuration, select the Automation tab.
Under the Step Automation tab, search for the Validate BeadChip Barcode automation.
Update the existing command line from python to python3 as follows.
Changes to the existing command line are in red.
/usr/bin/python3/opt/gls/clarity/extensions/conf/infinium/verifyBeadChipIDs.py -u {username} -p {password} -s {stepURI}
Select Save.

Update Existing Library Prep Routing Automation Script

This script only needs to be updated if you have the following workflows installed and want to route the artifact to the new MiSeq, NextSeq 500/550, NovaSeq 6000 v3, or NovaSeq 6000Dx workflows:

Library Prep Validation
Illumina DNA Prep (M) Tagmentation
Nextera Mate Pair
Nextera Rapid Capture Custom Enrichment
Nextera XT DNA
TruSeq ChIP-Seq
TruSeq DNA Exome
TruSeq DNA PCR-Free
TruSeq Custom Amplicon (TSCA)
TruSeq Methyl Capture EPIC
TruSeq Nano DNA
TruSeq Small RNA
TruSeq Stranded mRNA
TruSeq RNA Access
TruSeq RNA Exome
TruSight Tumor 170

Updated the script as follows.

From Configuration, select the Automation tab.
Under the Step Automation tab, search for the Routing script - Normalize Libraries automation for Normalize Libraries 1, Normalize Libraries 2, Normalize Libraries 3, or the Normalize Libraries (TruSight Tumor 170 v2.0.6) master step.
For Library Prep Validation, this automation is named Routing Script & Register Step Completed.
From the command line, search for --FIELD VALUE 'MiSeq' and update the WORKFLOW and STEP value from v3.1 to v3.2.
Search for --FIELD VALUE 'NextSeq' and update the WORKFLOW and STEP value from v1.0 to v1.1.
Search for --FIELD VALUE 'NovaSeq 3.0' and update the WORKFLOW and STEP value from v3.7 to v3.8.
Search for --FIELD VALUE 'NovaSeqDx' and update the WORKFLOW and STEP value from v1.1 to v1.2.

Release Notes

Last Updated: November 2024

Release Date: September 2023

Document Version: 2

These release notes describe the key changes to Illumina Preset Protocols (IPP) v2.6.

Compatibility

Refer to Compatibility under Instruments & Integrations.

New Features

Updated the non-IGA Python2 scripts to Python3. Symbolic links for Python 2 and 3 are removed from Clarity LIMS v6.2. All Python scripts are run under Python 3. If you have customized Python2 or 3 scripts in your existing workflows, then you must run them using the appropriate versions of Python (ie, Python2 or Python3).
Updated third-party dependency libraries.
Enabled the NovaSeq 6000 v3.8 workflow with CLPA.

Defects Fixed

Fixed the MiSeq sample sheet so that it now displays the pool name when the pool contains only one sample instead of the sample name. It also displays the well and plate information for submitted samples instead of for libraries.
Added missing PCR Product LIMSID custom field for CDC COVID-19 RT-PCR v1.0 workflow.
Fixed the bclfastq_reverse complement template so that it now uses the correct column name for the HIDE command.
Renamed the following protocol and workflow in AmpliSeq-Illumina-Immune-Repertoire-Panel:
- Standard Workflow (AmpliSeq for Illumina Response Panel v1.0) protocol to Standard Workflow (AmpliSeq for Illumina Repertoire Panel v1.0)
- Standard Workflow AmpliSeq for Illumina Immune Response Panel v1.0 workflow to Standard Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.0
Fixed workflow and step versions that were out of sync in the Nextera Rapid Capture Custom Enrichment workflow.
Fixed the Validate Flowcell Barcode automation (in the Load to Flowcell step of the NovaSeq Xp Protocol in the COIVDSeq workflow) so that it now accepts only uppercase alphanumeric characters in the first five positions of the barcode.
Fixed the non-IGA workflows so that they now show the Hide File Column Display and Manual File Attachment Method options under the File Column Options. The workflows previously showed the Hide File Column Display and Auto File Attachment Method options.

Known Issues

None

Revision History