Skip to content

Issues: broadinstitute/seqr-loading-pipelines

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

26 Open 293 Closed
26 Open 293 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Make sure load_data and download reference data use cached liftover files. bug
#1011 opened Jan 9, 2025 by bpblanken
Cache gene_id mappings w/ reference_data.
#1010 opened Jan 9, 2025 by bpblanken
Write remap errors and "all families failed" checks errors to validation errors files.
#1004 opened Dec 19, 2024 by bpblanken
@bpblanken
Investigate duplicate scores in dbnsfp, eigen, mitimpact, hmtvar, hgmd, splice_ai, topmed.
#993 opened Nov 27, 2024 by bpblanken
@bpblanken
Figure out how to get airflow to use pipeline-runner dataproc.
#943 opened Oct 29, 2024 by bpblanken
Deploy pipeline-runner on k8s.
#942 opened Oct 29, 2024 by bpblanken
Add pipeline-runner service account with appropriate permissions.
#941 opened Oct 29, 2024 by bpblanken
Add RunDataprocJobTask
#940 opened Oct 29, 2024 by bpblanken
@bpblanken
Add rsync of hail search data to luigi.
#939 opened Oct 29, 2024 by bpblanken
@bpblanken
1
Move dataproc spinup and spin down from airflow to luigi. Epic
#916 opened Oct 1, 2024 by bpblanken
@bpblanken
Re-think delivery of runs/metadata.json and runs/validation_errors.json.
#914 opened Sep 30, 2024 by bpblanken
1
Move sex checks out of data loading pipeline blocked Sex and Relatedness
#870 opened Aug 13, 2024 by lynnpais
Add strvctvre annotation. blocked Epic
#865 opened Aug 6, 2024 by bpblanken
@bpblanken
Add tests for the implemented migrations. Code Quality low priority
#862 opened Aug 5, 2024 by bpblanken
Pipeline should check the integrity of the metadata.json generated during a run. bug
#859 opened Aug 1, 2024 by bpblanken
1
Audit of Sample QC Genetic Ancestry Imputation on gnomAD v2+CMG vs gnomAD v4 Model Seqr Sample QC
#853 opened Jul 26, 2024 by matren395
@bpblanken @matren395
Modest Audit of DRAGEN Sample QC Outputs Seqr Sample QC
#852 opened Jul 26, 2024 by matren395
@matren395
Audit Sample QC Fields. Seqr Sample QC
#851 opened Jul 26, 2024 by bpblanken
@bpblanken @matren395
1
Map fields produced by seqr sample qc pipeline to UI fields in seqr. Seqr Sample QC
#849 opened Jul 26, 2024 by bpblanken
@bpblanken @matren395
Investigate support for running SpliceAi
#786 opened May 14, 2024 by lynnpais
@bpblanken
1
Migrate from nose to a different unittest provider Code Quality
#600 opened Oct 26, 2023 by bpblanken
@jklugherz
2
Port Seqr-Sample-QC into v03_pipeline Epic Seqr Sample QC v3 pipeline
#544 opened Jul 25, 2023 by bpblanken
@bpblanken
1
Add PrimAD reference data investigation Reference Data
#320 opened Mar 14, 2022 by hanars
@bpblanken
8
Add SQUIRLS in silico splice annotations blocked Reference Data v3 pipeline
#318 opened Mar 7, 2022 by anneodonnell
@bpblanken
4
Add consanguinity coefficient into pipeline Seqr Sample QC
#312 opened Mar 1, 2022 by mike-w-wilson
@bpblanken @matren395
1
ProTip! Mix and match filters to narrow down what you’re looking for.