Tapestri DNA Pipeline v1.8.4 and later supports demultiplexing of cells of only one sample at a time.
If multiple samples are sequenced in multiplex, the samples need to be demultiplexed based on their i7 indices prior to processing the data with Tapestri DNA Pipeline.
With V1 chemistry, each sample is linked to 2 pairs of fastq.gz files (2 unique i7 indices).
With V2 chemistry, each sample is linked to 1 pair of fastq.gz files (1 unique i5/i7 index pair).