Kb-python

Fix: Fixed how nascent/mature/ambiguous matrices are stored in anndata/loom files

Fix: The old lamanno workflow (for legacy purposes) should work now.

Anndata/loom files now have nascent/mature layers rather than unspliced/spliced layers.

--workflow=custom can take in multiple FASTA inputs

Allow --d-list to have comma-separated multiple FASTA files with URLs

Command-line options menu cleaned up a bit

Implements all the updates detailed in protocols paper: https://doi.org/10.1101/2023.11.21.568164

* kallisto version 0.50.1
* bustools version 0.43.1

General
* Bumped `ngs-tools>=1.7.3`.

`ref`
* **[DEPRECATION]** Split index generation using `-n` has been fully deprecated. (Thanks to amcdavid for catching a bug)

`count`
* Fixed a minor issue with `--workflow kite:10xFB`, where `bustools project` would be called before `bustools correct` (the order should be opposite). This fix required a bump to the `ngs-tools` dependency.
* Support for `--workflow lamanno` for `-x smartseq3`.
* **[DEPRECATION]** Counting using split indices by providing a comma-delimited list to `-i` has been fully deprecated.
* Support for whitelist (`-w option`) for `bulk`, `smartseq2` and `smartseq3` technologies.
* Added support for `-x 10XV3_ULTIMA`.

`count`
* Whitelist for technology `-x BDWTA` is now provided.