├── .gitignore ├── .pre-commit-config.yaml ├── .secrets.baseline ├── Authorization_URL_2020.jpg ├── Authorized URL.jpg ├── Jenkinsfile ├── LICENSE ├── LaunchPortal.jpg ├── LoggedInScreenshot.jpg ├── NOTICE ├── README.md ├── SandboxContainers.jpg ├── creds_setup.sh ├── datadictionary ├── LICENSE ├── NOTICE ├── README.md ├── design_notes.md ├── gdcdictionary │ ├── __init__.py │ ├── examples │ │ ├── invalid │ │ │ ├── aliquot_invalid_1.json │ │ │ ├── aliquot_invalid_2.json │ │ │ ├── aliquot_invalid_3.json │ │ │ ├── case_invalid_1.json │ │ │ └── case_invalid_2.json │ │ └── valid │ │ │ ├── acknowledgement.json │ │ │ ├── aligned_reads_index.json │ │ │ ├── aliquot.json │ │ │ ├── case.json │ │ │ ├── clinical_test.json │ │ │ ├── demographic.json │ │ │ ├── diagnosis.json │ │ │ ├── experiment.json │ │ │ ├── experimental_metadata.json │ │ │ ├── exposure.json │ │ │ ├── family_history.json │ │ │ ├── keyword.json │ │ │ ├── program.json │ │ │ ├── project.json │ │ │ ├── publication.json │ │ │ ├── read_group.json │ │ │ ├── read_group_qc.json │ │ │ ├── sample.json │ │ │ ├── slide.json │ │ │ ├── slide_count.json │ │ │ ├── slide_image.json │ │ │ ├── submitted_aligned_reads.json │ │ │ ├── submitted_copy_number.json │ │ │ ├── submitted_methylation.json │ │ │ ├── submitted_somatic_mutation.json │ │ │ ├── submitted_unaligned_reads.json │ │ │ └── treatment.json │ ├── schema_test.py │ └── schemas │ │ ├── README.md │ │ ├── _definitions.yaml │ │ ├── _settings.yaml │ │ ├── _terms.yaml │ │ ├── acknowledgement.yaml │ │ ├── aligned_reads_index.yaml │ │ ├── aliquot.yaml │ │ ├── case.yaml │ │ ├── clinical_test.yaml │ │ ├── core_metadata_collection.yaml │ │ ├── demographic.yaml │ │ ├── diagnosis.yaml │ │ ├── experiment.yaml │ │ ├── experimental_metadata.yaml │ │ ├── exposure.yaml │ │ ├── family_history.yaml │ │ ├── keyword.yaml │ │ ├── program.yaml │ │ ├── project.yaml │ │ ├── projects │ │ └── project1.yaml │ │ ├── publication.yaml │ │ ├── read_group.yaml │ │ ├── read_group_qc.yaml │ │ ├── sample.yaml │ │ ├── slide.yaml │ │ ├── slide_count.yaml │ │ ├── slide_image.yaml │ │ ├── submitted_aligned_reads.yaml │ │ ├── submitted_copy_number.yaml │ │ ├── submitted_methylation.yaml │ │ ├── submitted_somatic_mutation.yaml │ │ ├── submitted_unaligned_reads.yaml │ │ └── treatment.yaml └── setup.py ├── docker-compose.override.sample.yml ├── docker-compose.yml ├── docs ├── cheat_sheet.md ├── database_information.md ├── dev_tips.md ├── release_history.md ├── setup.md ├── useful_links.md └── using_the_commons.md ├── dump.sh ├── guppy_setup.sh ├── nginx.conf ├── scripts ├── arborist_setup.sh ├── fence_key_helper.py ├── fence_setup.sh ├── indexd_setup.sh ├── peregrine_setup.sh ├── postgres_always.sh ├── postgres_init.sql ├── postgres_run.sh ├── sheepdog_setup.sh ├── waitForContainers.sh └── wait_for_esproxy.sh ├── smoke_test.sh └── templates ├── config_helper.py ├── etlMapping.yaml ├── etl_creds.json ├── fence-config.yaml ├── gitops.json ├── guppy_config.json ├── indexd_creds.json ├── 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