- Adds the new `group` command to group PCR duplicates and return the groups in a tagged BAM file and/or flat file format. This was motivated by multiple requests to group PCR duplicated reads for downstream processes, e,g 45, 54. Special thanks to Nils Koelling (koelling) for testing the group command.
- Adds the `--umi-separator` option for `dedup` and `group` for workflow where `umi_tools extract` is not used to extract the UMI. This was motivated by 58