broadinstitute/seqr-loading-pipelines

Issues

• Audit/Reorganize v03_pipeline feature flags.

  #822 opened 6 days ago by bpblanken
  0

• Add `rsync` of hail search data to `luigi`.

  #939 opened 2 months ago by bpblanken
  1

• Export relatedness check to TSV

  #926 opened 19 days ago by lynnpais
  3

• Write remap errors and "all families failed" checks errors to validation errors files.

  #1004 opened 20 days ago by bpblanken
  0

• Re-architect `lookup` table (yet again!)

  #863 opened 5 months ago by bpblanken
  1

• Remove `high_constraint_region_mito`

  #846 opened a month ago by bpblanken
  2

• Import DRAGEN metrics file into v03 pipeline.

  #850 opened a month ago by bpblanken
  1

• Re-think delivery of `runs/metadata.json` and `runs/validation_errors.json`.

  #914 opened 3 months ago by bpblanken
  1

• 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 a month ago by bpblanken
  0

• Investigate duplicate scores in `dbnsfp`, `eigen`, `mitimpact`, `hmtvar`, `hgmd`, `splice_ai`, `topmed`.

  #993 opened a month ago by bpblanken
  0

• Add `RunDataprocJobTask`

  #940 opened 2 months ago by bpblanken
  0

• Add support for aneuploidy to the imputed sex validation.

  #906 opened a month ago by bpblanken
  1

• Handle `WriteMetadataForRun` caching bug.

  #962 opened 2 months ago by bpblanken
  0

• Add `CreateDataprocClusterTask`

  #938 opened 2 months ago by bpblanken
  0

• Update `metadata/validation_errors` to be single file, updated throughout pipeline.

  #944 opened 2 months ago by bpblanken
  1

• Figure out how to get `airflow` to use `pipeline-runner` dataproc.

  #943 opened 2 months ago by bpblanken
  0

• Deploy `pipeline-runner` on `k8s`.

  #942 opened 2 months ago by bpblanken
  0

• Add `pipeline-runner` service account with appropriate permissions.

  #941 opened 2 months ago by bpblanken
  0

• Move `dataproc` spinup and spin down from `airflow` to `luigi`.

  #916 opened 3 months ago by bpblanken
  0

• Clarify invalid allele validation.

  #919 opened 2 months ago by bpblanken
  1

• Improve the relatedness checking algorithm to also output clear relationships that are unexpected.

  #911 opened 2 months ago by bpblanken
  0

• VLM NOT

  #843 opened 2 months ago by lynnpais
  1

• Add `shellcheck` checking for bash scripts.

  #905 opened 2 months ago by bpblanken
  0

• Add `strvctvre` annotation.

  #865 opened 5 months ago by bpblanken
  0

• Move sex checks out of data loading pipeline

  #870 opened 5 months ago by lynnpais
  0

• Add tests for the implemented migrations.

  #862 opened 5 months ago by bpblanken
  0

• Ping hail search endpoint that reloads globals at the end of the pipeline.

  #892 opened 3 months ago by bpblanken
  1

• Move `_SUCCESS` file writing from `airflow` to `luigi`.

  #915 opened 3 months ago by bpblanken
  1

• Audit of Sample QC Genetic Ancestry Imputation on gnomAD v2+CMG vs gnomAD v4 Model

  #853 opened 5 months ago by matren395
  0

• Audit Sample QC Fields.

  #851 opened 5 months ago by bpblanken
  1

• Make `UpdatedCachedReferenceDatasetQuery` a dependency of `BaseUpdateVariantAnnotationsTableTask`.

  #907 opened 3 months ago by bpblanken
  1

• Manually modify composer ssd's to have `/seqr/seqr-hail-search-data` and `/seqr/seqr-reference-data` as root directories instead of `/ssd-datasets`.

  #891 opened 3 months ago by bpblanken
  1

• Create a simple http interface that responds to http POSTs and kicks off the v03_pipeline.

  #821 opened 3 months ago by bpblanken
  1

• Modify env vars in pipeline to be suffixed by `_DIR`

  #890 opened 3 months ago by bpblanken
  1

• `Delete` DAGs are failing to account for sample type in project table paths.

  #909 opened 3 months ago by bpblanken
  1

• Add automated docker builds to CI

  #848 opened 4 months ago by bpblanken
  1

• Create an updated pipeline-runner docker image that includes new VEP dependencies and v03_pipeline code.

  #820 opened 4 months ago by bpblanken
  2

• Delete ONT data

  #871 opened 5 months ago by lynnpais
  1

• Pipeline `complete()` needs to consider pedigree/remap information.

  #854 opened 5 months ago by bpblanken
  1

• Pipeline should check the integrity of the metadata.json generated during a run.

  #859 opened 5 months ago by bpblanken
  1

• Map fields produced by seqr sample qc pipeline to UI fields in seqr.

  #849 opened 5 months ago by bpblanken
  0

• Modest Audit of DRAGEN Sample QC Outputs

  #852 opened 5 months ago by matren395
  0

• Use the `ETag` of the clinvar submission and vcf to cache our gcs temp files.

  #823 opened 6 months ago by bpblanken
  2

• Family Table write needs to consider the pedigree when determining which families to update.

  #837 opened 6 months ago by bpblanken
  2

• Pipeline failed during allele registry step because of no response variants matching reference genome.

  #832 opened 6 months ago by bpblanken
  0

• Callset Import failure due to out of order keys.

  #828 opened 6 months ago by bpblanken
  3

• Add Ensembl -> Refseq lookup to "write_new_variants_table"

  #800 opened 6 months ago by bpblanken
  1

• Pedigree/S&R Cleanup

  #794 opened 7 months ago by bpblanken
  1

• Add `AlleleType` validation.

  #784 opened 7 months ago by bpblanken
  0

• Investigate support for running SpliceAi

  #786 opened 8 months ago by lynnpais
  1