├── .gitignore ├── LICENSE ├── README.md ├── instance-startup.sh └── lib ├── __init__.py ├── examples ├── README.md ├── __init__.py ├── api │ ├── __init__.py │ ├── bbt-DAG.py │ ├── container_scripts.py │ ├── containers.py │ ├── gdc-DAG.py │ ├── launch-bbt-DAG.sh │ ├── launch-gdc-DAG.sh │ └── steps.py ├── container_scripts │ ├── cghub.sh │ ├── fastqc.sh │ └── picard.sh ├── launch_scripts │ ├── startFastqc.sh │ └── tenBamFiles.txt └── utility_scripts │ ├── calculateDiskSize │ ├── constructCghubFilePaths │ ├── getChecksum │ └── getFilenames ├── isb-cgc-pipelines ├── pipelines ├── __init__.py ├── builder.py ├── config.py ├── data.py ├── db.py ├── logger.py ├── paths.py ├── queue.py ├── routes.py ├── schema.py ├── service.py └── utils.py └── scheduler ├── README.md ├── pipelineJobCanceller ├── pipelineJobScheduler └── receivePipelineVmLogs /.gitignore: -------------------------------------------------------------------------------- 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