Major updates - software versions, new wrappers, documentation

This release fixed issues brought up by users and at the same time updated the software versions to be more current.

Issues resolved

• #49 was addressed by adding to the documentation to clarify the SNP filtering step
• A comment was added to the Scrublet docs to account for some users needing to set the NUMBA_CACHE_DIR for #45
• annoy was downgraded to v1.15 to deal with some issues that were observed on some clusters with annoy 1.17 #44
• Wrapper scripts were introduced for checking the chromosome encoding in the bam, vcf and fasta files (where appropriate) to ensure they are the same; docs were updated to call these wrappers instead of the commands directly #39
• Docs were updated to fix the running code provided for Demuxalot from singularity exec Demuxafy.sif python Demuxalot.py ... to the correct call: singularity exec Demuxafy.sif Demuxalot.py ... #28
• Added a note about the usefulness of not including --SAMPLE_FILE in the AssignCellsToSamples to identify potential sample swaps #27

Software updates:

• R was updated to v4.4.0 (from 4.2.2)
• python to v3.9.7 (from 3.7.2)
• Seurat updated to v5.1.0
• Dropulation updated to v3.0.1 (from 2.5.4) which has more tools for implementing and demultiplexing
• Souporcell v2.5 (from v2) -> now supports hisat2 mapping and allows for implementation on newer python versions
• Demuxalot v0.4.1 (from 0.2.0) with help from @mschilli87 #46
• Note that solo was wrapped into scvi but I have not tested that version or identified how to alter the scripts to adapt to this change so the solo included here is the last solo version compatible with python 3.9 provided outside of scvi
• Update the scds R script to account for situations where there are less than 500 variable genes (by default it causes an error if not accounted for in bcds call)

Thanks to @mschilli87 for the help in identifying issues and helping resolve them.