TODOs as we head towards V1

[mschecht]

• Final report to conclude the run for user: number of cells, doublet rates, etc.
• Export aggregated metadata file from aggregated anndata for users who just want to work with it immediately
• Document default values for cell and gene QC explicitly!
• Run workflow over popular test datasets and narrate how to access the data e.g. 3K PBMC legacy workflow
  • Multiome
  • ATAC
  • GEX
• Implement Cell Ranger cluster-mode and figure out how to restart a job where it left off without snakemake destroying intermediate files.
• Double snapatac2 rule specific env
• Contact scverse and get feedback on the project
• Remove all steps after de-deduplication
• rename code base
• Feature requests:
  • cellranger multi
  • FLEX
  • TCR and BCR
• Feature request: confirm underlying tool versions to make sure they are compatible with sc-preprocess version