Illumina Connected Software

Manual Upgrade

This section describes the manual upgrade process from IPP v2.9 to IPP v2.10 to enable the changes described in Illumina Preset Protocols v2.10 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 include steps for:

  1. Updating the sequencing instrument presets and routing scripts to support the new MiSeq i100 Series cloud, MiSeq i100 Series on-premise and NovaSeq X Series on-premise integrations.

  2. Updating the precision of BP Aliquot Volume (ul) derived sample global field.

    ℹ BP Aliquot Volume (ul) field is used in Illumina Genomics Architecture - NovaSeq Sequencing v2.1, NovaSeq 6000 v3.8, NovaSeqDx v1.2 and NovaSeq X Series Sequencing v1.1 protocols in IPP v2.9.

  3. Updating the Library Prep Validation v2.3.4 protocol:

    • to display an expanded sample table under the Record Details milestone by default.

    • to route libraries to new instruments. Refer to these steps for updating the routing scripts.

  4. Updating the NovaSeq X Series Sequencing v1.1 protocol in IPP v2.9 to fix bugs. The steps involve updating container definition, step configuration, automations and global step fields. For manual upgrade instructions for the NovaSeq X Series Sequencing workflow, refer to NovaSeq X Series Integration v1.3.0 Manual Upgrade.

  5. Updating the NextSeq 500/550 Sequencing v1.2 protocol in IPP v2.9 to support generation of forward-orientation samplesheet that is compatible with NextSeq 500/550 Control Software Version 4.2 and Local Run Manager (LRM) v4.0 for selected applications. For manual upgrade instructions for the NextSeq 500/550 Sequencing workflow, refer to NextSeq 500/550 Integration v2.5.0 Manual Upgrade.

1. Update Sequencing Instrument Presets

In IPP v2.10, new workflows are available. New options for the MiSeq i100 Series (cloud), MiSeq i100 Series (on-premise) and NovaSeq X Series (on-premise) integrations have been added.

This can cause a conflict with the Sequencing Instrument derived sample custom field. The following workflows can be affected:

  • Illumina DNA Prep (M) Tagmentation v1.0.9

  • Nextera Mate Pair v1.0.10

  • Nextera XT DNA v2.0.10

  • TruSeq DNA PCR-Free v2.0.10

  • TruSeq Nano DNA v1.0.10

  • Library Prep Validation v2.3.4

  • TruSeq ChIP-Seq v1.0.10

  • TruSeq Methyl Capture EPIC v2.0.11

  • TruSeq Small RNA v1.0.10

  • TruSeq Stranded mRNA v2.1.10

  • TruSeq Custom Amplicon (TSCA) v1.0.10

  • Nextera Rapid Capture Custom Enrichment v2.0.11

  • TruSeq DNA Exome v2.0.10

  • TruSeq RNA Access v2.0.10

  • TruSight Tumor 170 v2.0.10

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)]:

Add New Options to Sequencing Instrument Global 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.

  3. For Additional Options, add the following to the Dropdown Items list:

    • NovaSeq X Series On-Prem

    • MiSeq i100 Series

    • MiSeq i100 Series On-Prem

Update Routing Script Automations

Existing library preparation workflows may include routing scripts to integrations. These routing scripts have been updated to add new options for the MiSeq i100 Series (cloud), MiSeq i100 Series (on-premise) and NovaSeq X Series (on-premise) integrations. Modify the automation script as follows.

  • [Optional] If you are using the MiSeq i100 Series (cloud) instrument, add the instrument to the script:

    \
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'MiSeq i100 Series' \
--WORKFLOW 'MiSeq i100 Series Sequencing v1.0' \
--STEP 'Assign Analysis Configuration Template (MiSeq i100 Series Sequencing v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'

  • [Optional] If you are using the MiSeq i100 Series (on-premise) instrument, add the instrument to the script:

    \
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'MiSeq i100 Series On-Prem' \
--WORKFLOW 'MiSeq i100 Series On-Prem Sequencing v1.0' \
--STEP 'Assign Analysis Configuration Template (MiSeq i100 Series On-Prem Sequencing v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'

  • [Optional] If you are using the NovaSeq X Series (on-premise) instrument, add the instrument to the script:

    \
--FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq X Series On-Prem' \
--WORKFLOW 'NovaSeq X Series On-Prem Sequencing v1.0' \
--STEP 'Assign Analysis Configuration Template (NovaSeq X Series On-Prem Sequencing v1.0)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'

  • [Optional] If you are using the NovaSeq X Series Sequencing workflow v1.2 for cloud, update the workflow version in the script:

    --FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NovaSeq X Series' \
--WORKFLOW 'NovaSeq X Series Sequencing v1.2' \
--STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.2)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\

  • [Optional] If you are using the NextSeq 500/550 Sequencing workflow v1.3, update the workflow version in the script:

    --FIELD_NAME 'Sequencing Instrument' \
--FIELD_VALUE 'NextSeq' \
--WORKFLOW 'NextSeq 500/550 Sequencing v1.3' \
--STEP 'Library Pooling (NextSeq 500/550 v1.3)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\

2. Update BP Aliquot Volume (ul) Global (Derived Sample) Field

  1. Select the Configuration tab, and then select the Custom Fields tab.

  2. Under Global Fields, navigate to the Derived Sample section and update BP Aliquot Volume (ul):

    • Decimal Places Displayed from 0 to 1

3. Update Library Prep Validation to Display Expanded Sample Table by Default

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

  2. Select Library Prep Validation workflow.

  3. Select Library Prep Validation protocol.

  4. Select Library Prep Validation step.

  5. Select Record Details milestone.

  6. Toggle Sample Display Default setting to Expand.

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