Hello everyone and thank you for this very much user friendly tool,

I found an error in the code as I wanted to install the maxatac data somewhere and followed the recommendations to update the default maxatac_data_path in constants.py.

However, the default path for chrom sizes and blacklist did not seem to update.

Error: Can't open genome file 
Error: The requested genome file (<myhome>/opt/maxatac/data/hg38/hg38.chrom.sizes) could not be opened. Exiting!<myhome>/opt/maxatac/data/hg38/hg38.chrom.sizes
. Exiting...
Error: Unable to open file <myhome>/opt/maxatac/data/hg38/hg38_maxatac_blacklist.bed. Exiting

After a bit of searching in the code I found that the error lied in the update_reference_genome_paths function in system.tools.py.

Indeed, the maxatac_data_path is redefined without taking into account the maxatac_data_path in constants.py.

To correct it, I only needed to remove the line and import maxatac_data_path from constants.py.