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31 Open 284 Closed
31 Open 284 Closed
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Issues list

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
Add rsync of hail search data to luigi.
#939 opened Oct 29, 2024 by bpblanken
Add code to seqr-pipeline to inject seqr's HAIL_SEARCH_DATA_DIR into the pipline as SEQR_APP_HAIL_SEARCH_DATA_DIR
#937 opened Oct 29, 2024 by bpblanken
@jklugherz
1
Export relatedness check to TSV
#926 opened Oct 15, 2024 by lynnpais
@jklugherz
3
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
Add support for aneuploidy to the imputed sex validation. enhancement
#906 opened Sep 23, 2024 by bpblanken
@jklugherz
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
Re-architect lookup table (yet again!) blocked optimization
#863 opened Aug 5, 2024 by bpblanken
1
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
Import DRAGEN metrics file into v03 pipeline. Seqr Sample QC
#850 opened Jul 26, 2024 by bpblanken
@bpblanken
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
Remove high_constraint_region_mito
#846 opened Jul 24, 2024 by bpblanken
@hanars
1
Audit/Reorganize v03_pipeline feature flags.
#822 opened Jun 25, 2024 by bpblanken
@bpblanken
Investigate support for running SpliceAi
#786 opened May 14, 2024 by lynnpais
@bpblanken
1
Refactor dataset CONFIG dict into models
#772 opened Apr 26, 2024 by jklugherz
1
Lint/Refactor the gencode download. Code Quality Good First Issue low priority v3 pipeline
#609 opened Oct 31, 2023 by bpblanken
@bpblanken
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