├── .dockerignore ├── .github └── workflows │ └── golangci-lint.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .secrets.baseline ├── .travis.yml ├── Docker ├── engine │ └── Dockerfile ├── s3Sidecar │ └── Dockerfile └── server │ └── Dockerfile ├── LICENSE ├── NOTICE ├── README.md ├── conformance ├── README.md └── cli.go ├── conformancelib ├── README.md ├── api.go ├── config.go ├── filter.go ├── input.go ├── loadTest.go ├── runTests.go ├── runTests_test.go ├── runner.go └── utils.go ├── database ├── constants.go ├── database.go ├── factory.go ├── models.go ├── psqldb_dao.go └── psqldb_test.go ├── docs ├── diagrams │ ├── components.svg │ └── graph.svg ├── how-to │ ├── deploy.md │ ├── retrieve_workflow_output.md │ ├── run_a_workflow.md │ └── write_and_run_workflow.md └── reference │ └── TechnicalDesignProposal.md ├── go.mod ├── go.sum ├── main.go ├── mariner ├── TECHDEBT.md ├── cleanup.go ├── command.go ├── config.go ├── engine.go ├── file.go ├── input.go ├── jobs.go ├── js.go ├── k8s.go ├── log.go ├── output.go ├── s3.go ├── scatter.go ├── server.go ├── token.go ├── tool.go ├── utility.go ├── workflow.go └── workflow_test.go ├── migrations ├── current_version ├── down ├── latest └── up ├── sidecar ├── README.md ├── constants.go ├── s3.go └── sidecar.go ├── testdata ├── commons_input_test │ ├── request_body.json │ └── workflow │ │ ├── cwl │ │ ├── gen3fuse_test.cwl │ │ ├── read_from_commons.cwl │ │ └── read_from_engine_workspace_and_commons.cwl │ │ ├── inputs.json │ │ ├── manifest.json │ │ └── workflow.json ├── no_input_test │ ├── request_body.json │ └── workflow │ │ ├── cwl │ │ ├── expressiontool_test.cwl │ │ ├── gen3_test.cwl │ │ ├── initdir_test.cwl │ │ ├── scatter_test.cwl │ │ └── subworkflow_test.cwl │ │ ├── inputs.json │ │ └── workflow.json └── user_data_test │ ├── request_body.json │ └── workflow │ ├── cwl │ ├── read_from_all.cwl │ ├── read_from_commons_and_user.cwl │ └── user-data_test.cwl │ ├── inputs.json │ ├── manifest.json │ └── workflow.json ├── version └── gitversion.go ├── wflib ├── README.md ├── pack.go ├── pack_test.go ├── schema.go ├── validate.go └── validate_test.go └── wftool ├── README.md ├── go.mod ├── go.sum └── main.go /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uc-cdis/mariner/HEAD/.dockerignore -------------------------------------------------------------------------------- /.github/workflows/golangci-lint.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uc-cdis/mariner/HEAD/.github/workflows/golangci-lint.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uc-cdis/mariner/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: 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