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mkdocs.yml
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site_name: Cromwell
site_url: http://www.software.broadinstitute.org/WDL
site_description: Cromwell documentation
site_author: Red Team at Broad Institute
repo_url: https://github.com/broadinstitute/cromwell/
nav:
- Introduction: index.md
- Tutorials:
# - Tutorial Map: tutorials/Overview.md
- Quick Introduction: tutorials/FiveMinuteIntro.md
- How to Configure Cromwell: tutorials/ConfigurationFiles.md
- Getting started with Google Cloud: tutorials/PipelinesApi101.md
- Getting started with Alibaba Cloud: tutorials/BCSIntro.md
- Getting started with AWS (beta): tutorials/AwsBatch101.md
- View the Timing Diagrams: tutorials/TimingDiagrams.md
- Persisting data between restarts: tutorials/PersistentServer.md
- Getting started on HPC Clusters: tutorials/HPCIntro.md
- Server Mode: tutorials/ServerMode.md
- Configuring the Local backend: tutorials/LocalBackendIntro.md
- Viewing Metadata: tutorials/MetadataEndpoint.md
- Getting started with Containers: tutorials/Containers.md
# - Introduction to Call Caching: tutorials/CallCaching101.md
# - Common Errors: tutorials/FrequentErrors.md
# - General Debugging Tips: tutorials/GeneralDebuggingTips.md
- Cromwell Basics:
- Modes: Modes.md
- Workflow Language Support: LanguageSupport.md
- Cromwell Releases: Releases.md
- Support: GettingHelp.md
- Command Line: CommandLine.md
- Feature Documentation:
- Call Caching: cromwell_features/CallCaching.md
- Labels: cromwell_features/Labels.md
- Hog Factors: cromwell_features/HogFactors.md
- Runtime Attributes: RuntimeAttributes.md
- Workflow Options:
- Overview: wf_options/Overview.md
- Google Cloud: wf_options/Google.md
- Workflow Optimizations:
- Optimizations: optimizations/optimizations.md
- "Task inputs: localization_optional": optimizations/FileLocalization.md
- "Volatile Tasks: volatile": optimizations/VolatileTasks.md
- "CheckpointFiles": optimizations/CheckpointFiles.md
- Configuration: Configuring.md
- Scaling / Horizontal Cromwell: Scaling.md
- Ecosystem: Ecosystem.md
- WOMtool: WOMtool.md
- Imports: Imports.md
- Sub-Workflows: SubWorkflows.md
- Execution: execution/ExecutionTwists.md
- Logging: Logging.md
- Backends:
- Overview: backends/Backends.md
- Local: backends/Local.md
- Google Cloud: backends/Google.md
- AWS Batch: backends/AWSBatch.md
- Alibaba Cloud: backends/BCS.md
- AWS Batch (beta): backends/AWS.md
- GA4GH TES: backends/TES.md
- HPC: backends/HPC.md
- Sun GridEngine: backends/SGE.md
- LSF: backends/LSF.md
- Slurm: backends/SLURM.md
- HTCondor: backends/HTcondor.md
- Filesystems:
- Overview: filesystems/Filesystems.md
- File Transfer Protocol (FTP): filesystems/FileTransferProtocol.md
- Google Cloud Storage: filesystems/GoogleCloudStorage.md
- HTTP: filesystems/HTTP.md
- Data Repository Service: filesystems/DataRepositoryService.md
- REST API:
- Overview: api/RESTAPI.md
- Errors: api/ErrorHandling.md
- For Developers:
- How to Build: developers/Building.md
- Architecture: developers/Arch.md
- Instrumentation: developers/Instrumentation.md
- Integration tests: developers/Centaur.md
- Security: developers/Security.md
- Contribute to docs: developers/Contribute.md
- CWL Parsing: developers/CwlParsing.md
- Bitesize Design Docs:
- Workflow Parsing & Graph Construction:
- What is WOM?: developers/bitesize/workflowParsing/whatIsWom.md
- From WDL Source to WOM:
- Overview: developers/bitesize/workflowParsing/wdlParsingOverview.md
- From WDL to WDLOM: developers/bitesize/workflowParsing/wdlToWdlom.md
- Adding new WDL Engine Functions: developers/bitesize/workflowParsing/engineFunctionAddition.md
- From CWL Source to WOM: developers/bitesize/workflowParsing/cwlParsingOverview.md
- Cromwell Actor System:
- High level view: developers/bitesize/majorActorSystem/5000FtActorSystem.md
- Workflow Execution:
- Main Actors: developers/bitesize/workflowExecution/majorActors.md
- Workflow, Subworkflow and Job Stores: developers/bitesize/workflowExecution/workflowSubworkflowAndJobStores.md
- Job Key / Value Store: developers/bitesize/workflowExecution/jobKeyValueStore.md
- Job retry decision logic: developers/bitesize/jobRetryLogic/jobRetryLogic.md
- Evaluating WDL expressions in WOM: developers/bitesize/workflowExecution/wdlExpressionEvaluation.md
- Execution and Value Stores:
- Execution Store: developers/bitesize/workflowExecution/executionStore.md
- Value Store: developers/bitesize/workflowExecution/valueStore.md
- Worked Examples: developers/bitesize/workflowExecution/executionAndValueStoreExamples.md
- IoActor: developers/bitesize/IoActor/IoActor.md
- Horizontal Cromwell ("Horicromtal"): developers/bitesize/horicromtal.md
- General Topics:
- Simpletons: developers/bitesize/general/simpletons.md
- Continuous Integration (CI) / Continuous Delivery (CD): developers/bitesize/ci/CICD.md
- Travis Centaur: developers/bitesize/ci/travis_centaur.md
theme: readthedocs
extra_css:
- css/extra.css
extra_javascript:
- js/extra.js
copyright: Copyright © 2019 <a href="https://broadinstitute.org">Broad Institute</a>
# google_analytics: ['identifierID', 'URL.org']