Match error-handling from nf-core (solves problem with status 140 that I had)

* implement groovy functions for samplesheet parsing

* set up utility class

* add build to map

* add json support

* rename json parser

* delete samplesheet module

* remove mount docs (deprecated)

* remove out.json from expected test output

* fix parsing vcf samplesheet

* fix report link and setup renv lockfile

* update dockerfile to use renv

* add license terms

* clarify custom scores + licenses

* drop small sampleset warning when integrating reference data

* drop aggregation

* update lockfile: drop data.table

* load scores the same way

* bump utils version

* drop effect_type (shouldn't actually be in columns array)

* use dev image

* update score test

* fix test

* bump pgscatalog_utils version

* boring but big: re-sync nf-core

* fix cache error in report

* nf-core resync

* set deno dir

* update schema

* set up auto-generated environment

* set workDir consistently

* improve caching

* fix help

* set outdir default

* use binary packages to build report image

* fix missing dependencies

* fix fraposa_pca

* add storeDir to relabel_ids

* fix score metadata in report

* store results permanently

* write to genotypes_cache, if set

* update conda

* add custom example scorefile

* Update schema to say what the cache is for

* Add information on cache and pipeline speed

* Not only for -resume

* fix storeDir

* fix tempdir on HPC/singularity

* gcp compatbility updates

* remove semantic structure from storeDirs (bad)

* Update cache.rst

* don't copy twice

* bump report singularity version

* fix quarto

* fix output

* fix fraposa

* fix capturing intersect counts

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Co-authored-by: smlmbrt <sam.a.lambert@gmail.com>

* Update plink2_makebed.nf

Remove chromosome so that it doesn't cause cache collision (should only run once per sampleset anyways)

* Fix prefix and output names

* Remove chromosome ID from orient

* stop using global variables

* use local variables

Add information about versions

* add version to report

* update author