Drop aggregation during report generation (#249)

* 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>

assets/examples/scorefiles/customgrch37.txt

@@ -0,0 +1,6 @@
+#pgs_name=testlift
+#trait_reported=test
+#genome_build=GRCh37
+chr_name	chr_position	effect_allele	other_allele	effect_weight
+1	4859488	A	G	-0.0504139458332669
+1	5297845	G	A	0.040436175688854

assets/examples/scorefiles/customgrch38.txt

@@ -0,0 +1,6 @@
+#pgs_name=test
+#trait_reported=test
+#genome_build=GRCh38
+chr_name	chr_position	effect_allele	other_allele	effect_weight
+1	4799428	A	G	-0.0504139458332669
+1	5237785	G	A	0.040436175688854