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[FEATURE] cellranger multi: leverage new reference-free VDJ option

Open tgelafr-pfzr opened this issue 1 month ago • 0 comments

Is your feature request related to a problem? Please describe

As of cellranger 10.0.0, VDJ analysis can be run reference free.

  • https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/inputs/cr-multi-config-csv-opts#vdj
  • Release notes

This functionality should be exposed in the cellranger multi module.

Describe the solution you'd like

We should parse this option from the meta_vdj input and modify the config file appropriately. We should also include the VDJ section in the config file if no reference is provided as long as this denovo flag is set and it's not a multiplexed experiment.

Describe alternatives you've considered

No response

Additional context

No response

tgelafr-pfzr avatar Nov 17 '25 21:11 tgelafr-pfzr