implement bambu.singlecell / bambu.spatial function as a wrapper to call bambu in single cell or spatial mode

[ch99l]

• group related single-cell parameters into opt.singlecell list argument

• write bambu.singlecell() & bambu.spatial() function wrapper to run bambu in single-cell mode:

  • use the basic parameters (data, transcript discovery, transcript quantification) with opt.singlecell argument
  • wrap the code in Custom single-cell and spatial section in the main documentation in devel_pre_v4 under bambu.singlecell() call (we expect users only have to run one bambu.singlecell() to get the output instead of running multiple lines of code)

• update arguments related to the issue:

  • demultiplexed (automatically set to TRUE in bambu.singlecell())
    • remove the option to provide reads-to-barcode mappng .csv file
    • rename with extractBarcodeUMI
  • clusters (include in opt.singlecell)
    • fix bug when provided as a barcode-to-cluster csv file (do we need that actually?)
  • dedupUMI (include in opt.singlecell)
    • nothing to change, to be included as an element in opt.singlecell list for bambu.singlecell() call
  • barcodesToFilter, sampleName, cleanReads
    • remove the parameters