Sample Sheet and Run Recipe File Generation

Sample sheet and run recipe file generation occurs on the step before the run—Dilute and Denature (NovaSeq 6000 v2.2) in the NovaSeq Standard protocol or Load to Flowcell (NovaSeq 6000 v2.2) in the NovaSeq Xp protocol. This step is where samples are placed on the library tube or flow cell that is loaded in the NovaSeq instrument.

In the default configuration, the Generate Sample Sheet and Run Recipe automation generates the following:

• One CSV format sample sheet file for use bcl2fastq v2.20 downstream analysis
• One JSON format run recipe file

The Prepare Files for NovaSeq automation places the generated files on the NAS where the instrument uses them to start the run.

• The Prepare Files for NovaSeq automation command line invokes the copy_attachments_to_network_folder script in novaseq-remote-extensions.jar. The script can be used on a remote AI node/automation worker, in case the Clarity LIMS server does not have direct access to the NAS.
• The output folder for the run recipe file is found in the novaseq.runSetupFolder property.
• The output folder for the sample sheet is determined by using the novaseq.sampleSheetPathSearchReplaceSuffixes property. This property must contain exactly one suffix (not a comma-separated list) to derive a full property name based on novaseq.sampleSheetPathPrefixReplace.

The contents of the sample sheet are controlled by the following fields configured on the Dilute and Denature (NovaSeq 6000 v2.2) and Load to Flowcell (NovaSeq 6000 v2.2) steps:

• Experiment Name
• Read 1 Cycles
• Read 2 Cycles
• Workflow
• Reverse Complement Workflow
• Read1UMILength
• Read2UMILength
• Read1StartFromCycle
• Read2StartFromCycle

See the Bcl2fastq2 Sample Sheet Generation section of the Illumina Instrument Sample Sheets (NGS v5.17 & later) document for detailed information on the following:

• Sample sheet generation script parameters and usage
• Sample sheet data and configuration options
• Enabling unique FASTQ file names per sequencing run

The contents of the run recipe are controlled by the following fields. These fields are configured on the Dilute and Denature (NovaSeq 6000 v2.2) and Load to Flowcell (NovaSeq 6000 v2.2) steps.

• Experiment Name
• Run Mode
• Workflow Type
• Sample Loading Type (populated based on Workflow field)
• Paired End
• Read 1
• Read 2
• Index Read 1
• Index Read 2
• Sample Sheet Path
• BaseSpace Configuration
• Use Custom Read 1 Primer
• Use Custom Read 2 Primer
• Use Custom Index Read 1 Primer

The following fields are also included in the run recipe:

• Library Tube Barcode (librarytube_ID in JSON file)
– NovaSeq Standard workflow—Library tube barcode is derived from the container name entered or scanned on the Placement screen.
– NovaSeq Xp workflow—Library tube barcode is derived from the Library Tube Barcode field in the Load To Flowcell (NovaSeq 6000 v2.2) step.
• Flowcell Barcode (flowcell_ID in JSON file)
– NovaSeq Standard workflow—Library tube barcode is not output to JSON recipe file.
– NovaSeq Xp workflow—Flow cell barcode is derived from the container name entered or scanned on the Placement screen.
• Rehyb—preset to False.
• Output Folder (output_folder in JSON file)—Derived from the system property novaseq.seqservice.netPathPrefixSearch.
• Attachment—Derived from the system property novaseq.sampleSheetPathPrefixSearch with the name of the sample sheet added to the end of the path.
• Use BaseSpace (use_basespace in JSON file)—Set to False if the BaseSpace Sequence Hub Configuration step field value is Not Used, and true otherwise.
• The sample sheet and run recipe files are mandatory inputs for the AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.2) step. For the automated run to start successfully, select the Generate Sample Sheet and Run Recipe button to generate these files.
• The output folders must exist on the system where the script runs (can be a remote AI node/automation worker).
• The output folders must be writable by the glsai user.