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

⚠️ Users that use Python in their scripts must upgrade to IPP v2.6. For more information, contact Illumina Support.

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

1. From Configuration, select the Automation tab.

2. Under the Step Automation tab, search for the Validate Flowcell Barcode automation.

3. 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}"

4. Select Save.

5. From Configuration, select the Automation tab.

6. Under the Step Automation tab, search for the CovidSEQ: Parse TSV Run Report automation.

7. 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}

8. Select Save.

Update CDC Covid 19 RT PCR Workflows

1. 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

   
2. 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}

3. 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.

1. From Configuration, select the Automation tab.

2. Under the Step Automation tab, search for the Validate BeadChip Barcode 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/infinium/verifyBeadChipIDs.py -u {username} -p {password} -s {stepURI}

4. 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.

1. From Configuration, select the Automation tab.

2. 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.

3. From the command line, search for --FIELD VALUE 'MiSeq' and update the WORKFLOW and STEP value from v3.1 to v3.2.

   ℹ️ This update is required if the user wants to route to the MiSeq Sequencing v3.2 workflow that can be installed from IPP v2.6.

4. Search for --FIELD VALUE 'NextSeq' and update the WORKFLOW and STEP value from v1.0 to v1.1.

   ℹ️ This update is required if the user wants to route to the NextSeq 500/550 Sequencing v1.1 workflow that can be installed from IPP v2.6.

5. Search for --FIELD VALUE 'NovaSeq 3.0' and update the WORKFLOW and STEP value from v3.7 to v3.8.

   ℹ️ This update is required if the user wants to route to the NovaSeq 6000 v3.8 workflow that can be installed from IPP v2.6.

6. Search for --FIELD VALUE 'NovaSeqDx' and update the WORKFLOW and STEP value from v1.1 to v1.2.

   ℹ️ This update is required if the user wants to route to the NovaSeq 6000Dx v1.2 workflow that can be installed from IPP v2.6.