├── .gitignore ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── bin └── dockerflow ├── examples ├── gatk │ ├── GatkPairedSingleSample.java │ ├── GatkPairedSingleSampleAlt.java │ ├── README.md │ ├── gatk-args.yaml │ └── gatk-workflow.yaml └── hello │ ├── HelloWorkflow.java │ ├── README.md │ ├── hello-args.yaml │ └── hello-workflow.yaml ├── pom.xml └── src ├── main └── java │ └── com │ └── google │ └── cloud │ └── genomics │ └── dockerflow │ ├── Dockerflow.java │ ├── DockerflowConstants.java │ ├── args │ ├── ArgsBuilder.java │ ├── ArgsTableBuilder.java │ ├── TaskArgs.java │ └── WorkflowArgs.java │ ├── dataflow │ ├── DataflowBuilder.java │ └── DataflowFactory.java │ ├── runner │ ├── Operation.java │ ├── TaskException.java │ └── TaskRunner.java │ ├── task │ ├── Task.java │ ├── TaskBuilder.java │ └── TaskDefn.java │ ├── transform │ ├── BreakFusion.java │ ├── DeleteIntermediateFiles.java │ ├── DockerDo.java │ ├── MergeBranches.java │ └── WaitForOperation.java │ ├── util │ ├── FileUtils.java │ ├── HttpUtils.java │ └── StringUtils.java │ └── workflow │ ├── GraphItem.java │ ├── Workflow.java │ ├── WorkflowDefn.java │ └── WorkflowFactory.java └── test ├── java └── com │ └── google │ └── cloud │ └── genomics │ └── dockerflow │ ├── DockerflowITCase.java │ ├── DockerflowTest.java │ ├── TestUtils.java │ ├── args │ └── ArgsTableBuilderTest.java │ ├── dataflow │ └── DataflowFactoryTest.java │ └── examples │ ├── ComplexGraph.java │ ├── ExampleGraphsITCase.java │ ├── ExampleGraphsTest.java │ ├── LinearGraph.java │ └── MultiLinearGraph.java └── resources ├── branching-graph.yaml ├── complex-graph.yaml ├── cwl-graph.yaml ├── folder-copy.yaml ├── gather-graph.yaml ├── input-one.txt ├── input-two.txt ├── linear-graph.yaml ├── output-one.txt ├── parallel-graph.yaml ├── param-sub.yaml ├── reordered-graph.yaml ├── task-one.yaml ├── task-two.yaml ├── test-folder ├── file1.txt └── file2.txt ├── workflow.yaml └── workflowArgs.csv /.gitignore: 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