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An important consideration when analyzing UMI data are the errors introduced into the UMIs themselves during PCR amplification of the original molecule. If these errors are not accounted for and each sequenced UMI is considered to be representative of the original UMI, the number of unique molecules can be significantly overestimated. To account for this, the UMI deduplication task the Deduplicate UMIs task uses an implementation of the UMI-tools algorithm described in Smith et al. 2017.  

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Retain only one alignment per UMI

Deduplicate UMIs has  has an alternative setting to more closely match methods used by CellRanger: Retain only one alignment per UMI. Selecting this option changes how the task functions and requires that you specify the genome assembly and gene/feature annotation.

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