[FEATURE] cellranger multi: leverage new reference-free VDJ option
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Description
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
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Inspect the cellranger multi module, its meta_vdj input handling, and the generated config file. Start by tracing how VDJ reference settings are parsed, then verify the denovo case: include the VDJ section without a reference only for non-multiplexed experiments, and confirm the option is represented in the resulting configuration.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100