mkdocs.yml

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
- 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

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