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broadinstitute
/
seqr-loading-pipelines
hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
MIT License
22
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20
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add allele registry step in update vat with samples task
#745
jklugherz
closed
5 months ago
1
make old crdq runnable
#744
jklugherz
closed
5 months ago
0
Revert "delete old crdq code"
#743
jklugherz
closed
5 months ago
0
try moving clinvar submitter tmp file to gcs before importing
#742
jklugherz
closed
5 months ago
0
add some logging for crdq debugging
#741
jklugherz
closed
5 months ago
0
Better isolate dev/prod pipeline runs
#740
bpblanken
closed
3 months ago
0
clinvar submitters and conditions
#739
jklugherz
closed
5 months ago
0
delete old crdq code
#738
jklugherz
closed
5 months ago
0
Dev
#737
bpblanken
closed
5 months ago
0
Lookup table touchups
#736
bpblanken
closed
5 months ago
0
fix MITO clinvar crdq
#735
jklugherz
closed
5 months ago
0
Improve Family Table copying on pod startup.
#734
bpblanken
closed
5 months ago
2
make WriteCachedReferenceDatasetQuery importable
#733
jklugherz
closed
5 months ago
0
Fix clinvar prefilter fields
#732
bpblanken
closed
6 months ago
0
Fix optional fields union
#731
bpblanken
closed
6 months ago
0
resolve parent being parsed as aunt/nephews bug
#730
bpblanken
closed
5 months ago
1
Improve type validation during callset importing.
#729
bpblanken
closed
2 months ago
0
Dev
#728
bpblanken
closed
6 months ago
0
Sex and relatedness bugfixes
#727
bpblanken
closed
6 months ago
0
merge crdq wrapper task to dev
#726
jklugherz
closed
6 months ago
0
DRAGEN has haploid calls?
#725
bpblanken
closed
4 months ago
5
crdq wrapper task
#724
jklugherz
closed
6 months ago
4
use dataset configs in UpdateVATWithUpdatedRDC complete() take 2
#723
jklugherz
closed
6 months ago
0
bugfix for project table updates
#722
bpblanken
closed
6 months ago
0
use datasets in Globals constructors
#721
jklugherz
closed
6 months ago
0
Dev
#720
bpblanken
closed
6 months ago
0
better sex and relatedness enablement
#719
bpblanken
closed
6 months ago
0
use dataset configs in UpdateVATWithUpdatedRDC complete()
#718
jklugherz
closed
6 months ago
0
main <- dev
#717
bpblanken
closed
6 months ago
0
migration
#716
bpblanken
closed
5 months ago
0
add a few more logs
#715
jklugherz
closed
6 months ago
0
Improve logging.
#714
bpblanken
closed
6 months ago
0
add new clinvar pathogenicity and contig filter workaround
#713
jklugherz
closed
6 months ago
0
fix version mismatch error message
#712
jklugherz
closed
6 months ago
0
prefer env vars for vep path
#711
bpblanken
closed
6 months ago
0
main <- dev
#710
bpblanken
closed
6 months ago
0
bump hail version to 0.2.128
#709
jklugherz
closed
6 months ago
1
Upgrade hail to 0.2.128
#708
jklugherz
closed
6 months ago
0
fix test tables for new clinvar assertions
#707
jklugherz
closed
6 months ago
3
fix contig recoding for 37
#706
jklugherz
closed
6 months ago
0
allow luigi worker logs to come through
#705
jklugherz
closed
6 months ago
0
Add 'reasons' key to `metadata.json` with sex/relatedness check failures.
#704
bpblanken
closed
6 months ago
0
Bump orjson from 3.9.10 to 3.9.15
#703
dependabot[bot]
closed
6 months ago
0
Add reference genome check to VEP.
#702
bpblanken
closed
6 months ago
0
Delete old pipeline runs.
#701
bpblanken
closed
6 months ago
1
Lookup table refactor.
#700
bpblanken
closed
5 months ago
0
Bump cryptography from 42.0.0 to 42.0.4
#699
dependabot[bot]
closed
6 months ago
0
mito dataset changes
#698
jklugherz
closed
6 months ago
0
Run ruff format during CI.
#697
bpblanken
closed
6 months ago
0
add UpdatedCachedReferenceDatasetQuery
#696
bpblanken
closed
6 months ago
1
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