Manual Upgrade

This section describes the manual upgrade process from IPP v2.11 to IPP v2.12 to enable the changes described in Illumina Preset Protocols v2.12 Release Notes. If you do not want to upgrade the latest workflow through IPP, then update the workflow configuration manually using the following information.

Conflicts may occur for the following scenarios when upgrading to IPP v2.12:

1. For previous IPP version, one or more library preparation workflows have been imported.
2. Sequencing Instrument (derived sample global custom field) is already existing in the Clarity LIMS instance
3. NovaSeq X Series Flowcell Type (derived sample global custom field) is already existing in the Clarity LIMS instance

The manual upgrade instructions include steps for supporting the new NovaSeq X Series Sequencing v2.0 workflow:

1. Update existing Sequencing Instrument derived sample global custom field and routing scripts to route libraries to the new workflow.
2. Resolve conflict of existing NovaSeq X Series Flowcell Type derived sample global custom field

1. Update Existing Sequencing Instrument (Derived Sample Global Custom Field) and Routing Scripts to Route Libraries to the New NovaSeq X Series Sequencing v2.0 Workflow

In IPP v2.12, new workflow for NovaSeq X Series is available. The options for Sequencing Instrument derived sample global custom fields have been updated to support the new workflow.

This can cause a conflict with the Sequencing Instrument derived sample global custom field for the following workflows:

• Illumina DNA Prep (M) Tagmentation v1.0.11
• Nextera Mate Pair v1.0.12
• Nextera XT DNA v2.0.12
• TruSeq DNA PCR-Free v2.0.12
• TruSeq Nano DNA v1.0.12
• Library Prep Validation v2.3.7
• TruSeq ChIP-Seq v1.0.12
• TruSeq Methyl Capture EPIC v2.0.13
• TruSeq Small RNA v1.0.12
• TruSeq Stranded mRNA v2.1.12
• TruSeq Custom Amplicon (TSCA) v1.0.12
• Nextera Rapid Capture Custom Enrichment v2.0.13
• TruSeq DNA Exome v2.0.12
• TruSeq RNA Access v2.0.12
• TruSight Tumor 170 v2.0.12

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)]:

Remove Existing Options in Existing Sequencing Instrument (Derived Sample Global Custom 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 under Derived Sample.
3. Both NovaSeq X Series Integration and NovaSeq X Series On-Prem Integration shall use the new updated NovaSeq X Series Sequencing v2.0 workflow. Remove the redundant option NovaSeq X Series On-Prem from the Dropdown Items list.

Update Routing Script Automations

Existing library preparation workflows (such as Library Prep Validation v2.3.5) may include routing scripts to integrations. Update these routing scripts to route to the new NovaSeq X Series Sequencing v2.0 workflow. Modify the automation script as follows.

• [Optional] If you are using the NovaSeq X Series instrument, update the WORKFLOW and STEP parameters of the routing script:

  \
  --FIELD_NAME 'Sequencing Instrument' \
  --FIELD_VALUE 'NovaSeq X Series' \
  --WORKFLOW 'NovaSeq X Series Sequencing v2.0' \
  --STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v2.0)' \
  --INPUTS_OR_OUTPUTS 'OUTPUTS'

2. Resolve Conflict of Existing NovaSeq X Series Flowcell Type (Derived Sample Global Custom Field)

The new NovaSeq X Series Sequencing v2.0 workflow supports the new NovaSeq X Series 5B flowcells. Conflict is expected if the new workflow version is installed on a Clarity LIMS instance with an earlier version of NovaSeq X Series Sequencing workflow.

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 NovaSeq X Series Flowcell Type under Derived Sample.
3. For Additional Options, add the following to the Dropdown Items list:

   • 5B