Add single-cell analysis functionality

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

Start by reviewing the pipeline and its design file, then compare the linked plate_scATAC-seq Snakefile for single-cell processing. Done means a --single-cell option supports merging samples for peak calling and projecting single-cell alignments onto the merged peaks, with downstream analysis addressed.