The Wrapper.py script should run the analysis for IGL, TCR, and IGH loci. These scripts are meant for R2C2 data and haven't been used for anything else. All your fasta and subread files for each cell should be in the same folder. Aligned reads in sam format should be in a different format. The help message of Wrapper.py should point you towards everything you need.
If you need help running this please email me at [email protected]. There is a select few people for whom this repository might be useful so I'd much rather walk you through it then write 15 pages of a how-to.