How to reuse cached data

What is the cache?

See here for more details about what the genotypes cache is.

Just add the --genotype_cache_zip parameter after you've calculated a score for the first time:

$ nextflow run pgscatalog/pgsc_calc \
  -r v3-alpha.1 \
  --input samplesheet.csv \
  --target_build GRCh38 \
  --genotype_cache_zip <PATH/TO/genotypes.zarr.zip>

This can significantly speed up the PGSC_CALC_LOAD processes depending on the number of successful cache hits.

When the calculation job finishes a new cache will be published in the results directory, containing previously uncached variants.

tip

The cache is compressed but can grow to be quite large. If you want to disable creating and publishing the cache add a parameter to your run:

--publish_cache false