├── .gitignore ├── DatabaseRestApi ├── app │ ├── Dockerfile │ ├── requirements.txt │ ├── run.py │ └── settings.py ├── mongo-seed │ ├── .DS_Store │ ├── Dockerfile │ └── driver_db_dump.json └── notebooks │ └── biograph_seeding_02_CollectMyDrugFromSource.ipynb ├── LICENSE ├── README.md ├── ReportingApplication ├── Dockerfile ├── GRCh38_01-Jan-2019-ClinicalEvidenceSummaries.txt ├── Singularity.report ├── clinicalreporting_docxtemplater │ ├── .DS_Store │ ├── .gitignore │ ├── README.md │ ├── data │ │ ├── .DS_Store │ │ └── template.docx │ ├── example.sh │ ├── main.js │ ├── package-lock.json │ └── package.json ├── driver_db_dump.json ├── inout │ ├── strelka_passed_missense_somatic_snvs.vcf │ └── strelka_passed_missense_somatic_snvs_metadata.json ├── make_report.sh ├── reporting.R └── vep_docker.ini ├── VepFileDeployment ├── Dockerfile.GRCh37 ├── Dockerfile.GRCh38 ├── README.md ├── Singularity.filedeploy └── copy_data.sh ├── doc ├── PipelineWiki.md ├── PipelineWorkflow.jpeg ├── 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