Add single-cell analysis functionality

[drpatelh]

Should be possible to add a --single-cell parameter to the pipeline that processes the data accordingly. I would imagine that you just set the replicate id in the design file to 1 for all the samples. This will then merge all of the samples together to create a "bulk" sample to call the peaks. The data from the single-cell alignments will then need to be projected onto the merged peaks. Will need to look into the analysis downstream from that but the pipeline should already have most of the functionality.

Another pipeline written in Snakemake:
https://github.com/dbrg77/plate_scATAC-seq/blob/master/mSp_scATAC-seq/Snakefile

Other tools:
https://omictools.com/single-cell-atac-seq-analysis-category