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Drop aggregation during report generation #249

Merged
merged 48 commits into from
Feb 29, 2024
Merged

Drop aggregation during report generation #249

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6ca396d
drop small sampleset warning when integrating reference data
nebfield Feb 21, 2024
00ef345
drop aggregation
nebfield Feb 21, 2024
e352c6d
update lockfile: drop data.table
nebfield Feb 21, 2024
156eb7a
load scores the same way
nebfield Feb 21, 2024
413cd46
bump utils version
nebfield Feb 21, 2024
0d7cfcf
drop effect_type (shouldn't actually be in columns array)
nebfield Feb 21, 2024
be44734
use dev image
nebfield Feb 22, 2024
7dfc747
update score test
nebfield Feb 22, 2024
7abbb99
fix test
nebfield Feb 22, 2024
bc2bc0f
bump pgscatalog_utils version
nebfield Feb 22, 2024
4904df7
boring but big: re-sync nf-core
nebfield Feb 21, 2024
800b918
fix cache error in report
nebfield Feb 22, 2024
ecba806
nf-core resync
nebfield Feb 22, 2024
23b3710
set deno dir
nebfield Feb 22, 2024
9ac3954
update schema
nebfield Feb 22, 2024
6b209d1
set up auto-generated environment
nebfield Feb 22, 2024
bff64bb
set workDir consistently
nebfield Feb 22, 2024
d9dd9e9
improve caching
nebfield Feb 22, 2024
05ae2fb
fix help
nebfield Feb 22, 2024
eb6624c
set outdir default
nebfield Feb 22, 2024
af0e870
Merge pull request #250 from PGScatalog/resyncnf
nebfield Feb 22, 2024
dde2899
use binary packages to build report image
nebfield Feb 22, 2024
7d36cf4
fix missing dependencies
nebfield Feb 22, 2024
9b13478
fix fraposa_pca
nebfield Feb 23, 2024
c1af46e
add storeDir to relabel_ids
nebfield Feb 23, 2024
35dfda2
fix score metadata in report
nebfield Feb 23, 2024
35bf2e2
store results permanently
nebfield Feb 23, 2024
f1efe7c
write to genotypes_cache, if set
nebfield Feb 23, 2024
fdfd1cf
update conda
nebfield Feb 23, 2024
6786404
add custom example scorefile
nebfield Feb 23, 2024
26d4d82
Update schema to say what the cache is for
smlmbrt Feb 26, 2024
fd4ba44
Add information on cache and pipeline speed
smlmbrt Feb 26, 2024
b4c8ea1
Not only for -resume
smlmbrt Feb 26, 2024
a38dffd
fix storeDir
nebfield Feb 26, 2024
cc18006
fix tempdir on HPC/singularity
nebfield Feb 27, 2024
b119fb9
gcp compatbility updates
nebfield Feb 27, 2024
0af97f8
remove semantic structure from storeDirs (bad)
nebfield Feb 28, 2024
fbf9b84
Merge branch 'drop-report-aggregation' into fix-cloud
nebfield Feb 28, 2024
86d947f
Update cache.rst
smlmbrt Feb 28, 2024
279496c
Merge branch 'drop-report-aggregation' into docs_cache
nebfield Feb 28, 2024
f433dd1
Merge pull request #254 from PGScatalog/docs_cache
nebfield Feb 28, 2024
8628fa8
Merge pull request #256 from PGScatalog/fix-cloud
nebfield Feb 28, 2024
9f23ced
don't copy twice
nebfield Feb 28, 2024
1c77f90
bump report singularity version
nebfield Feb 28, 2024
3c918cc
fix quarto
nebfield Feb 28, 2024
fae1e03
fix output
nebfield Feb 29, 2024
acd124f
fix fraposa
nebfield Feb 29, 2024
c3b58ba
fix capturing intersect counts
nebfield Feb 29, 2024
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Empty file added assets/NO_FILE_INTERSECT_COUNT
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6 changes: 6 additions & 0 deletions assets/examples/scorefiles/customgrch37.txt
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Original file line number Diff line number Diff line change
@@ -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
6 changes: 6 additions & 0 deletions assets/examples/scorefiles/customgrch38.txt
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Original file line number Diff line number Diff line change
@@ -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
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