File caching

StemCNV-check generates a cache folder (default: ~/.cache/stemcnv-check), where re-usable files that are not (necessarily) project specific are saved for re-use. The location of the cache can be changed through the config file or with the --cache-path command line option.

The cache includes:

• Genome reference files (fasta, gtf)

• Array specific static data files (for easy re-use between projects)

• conda environments generated and used by snakemake

• apptainer images generated and used by snakemake