3.2

Key changes

1) Support for two-round barcoding workflows

Demultiplexing can now include two rounds of lima demultiplexing.

2) Parameter YAML model updates for runs/samples/barcodes

The YAML parameters now have a separate barcodes section and support for optional second-round barcode IDs.

Key user-facing YAML fields to review when upgrading:

• runs[].run_id
• runs[].reads_file
• runs[].samples[].barcode_ids
• runs[].samples[].barcode_ids_round2 (new for round2 demux)
• barcodes[].barcode_id
• barcodes[].barcode
• lima_supplemental_settings
• lima_round2_supplemental_settings

3) Barcode BAM tags are now a key part of interpretation (bc, bq)

bc (barcode pair index tag) is propagated to downstream tables. For two-round demultiplexing, reported bc values correspond to the last demultiplexing round.