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mkdocs.yml
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site_name: Bpipe
repo_url: https://github.com/ssadedin/bpipe
logo: icon.png
theme:
name: mkdocs
highlightjs: true
hljs_languages:
- yaml
- groovy
extra_css: [extra.css]
nav:
- Overview:
- Introduction: Overview/Introduction.md
- Comparison To Workflow Tools: Overview/ComparisonToWorkflowTools.md
- Install Instructions: Overview/InstallInstructions.md
- Language:
- About: Language/About.md
- Check: Language/Check.md
- Chr: Language/Chr.md
- Cleanup: Language/CleanupStatement.md
- Config: Language/Config.md
- Debug: Language/Debug.md
- Directories: Language/Directories.md
- Doc: Language/Doc.md
- Exec: Language/Exec.md
- Fail: Language/Fail.md
- File: Language/File.md
- Filter: Language/Filter.md
- Forward: Language/Forward.md
- From: Language/From.md
- Glob: Language/Glob.md
- Grep: Language/Grep.md
- Load: Language/Load.md
- Merge Point Operator: Language/MergePoints.md
- Multi: Language/Multi.md
- Output: Language/Output.md
- Options: Language/Options.md
- Prefix: Language/Prefix.md
- Produce: Language/Produce.md
- R: Language/R.md
- Segments: Language/Segments.md
- Send: Language/Send.md
- Succeed: Language/Succeed.md
- Transform: Language/Transform.md
- Using: Language/Using.md
- Preserve in pipeline: Language/PreserveInPipeline.md
- requires: Language/requires.md
- uses: Language/uses.md
- var: Language/var.md
- Commands:
- Using the bpipe command: Commands/Commands.md
- cleanup: Commands/cleanup.md
- execute: Commands/execute.md
- history: Commands/history.md
- jobs: Commands/jobs.md
- log: Commands/log.md
- preserve: Commands/preserve.md
- query: Commands/query.md
- retry: Commands/retry.md
- run: Commands/run.md
- status: Commands/status.md
- stop: Commands/stop.md
- test: Commands/test.md
- Tutorials:
- Hello, World: Tutorials/Hello-World.md
- Example With Inputs And Outputs: Tutorials/ExampleWithInputsAndOutputs.md
- Real Pipeline Tutorial: Tutorials/RealPipelineTutorial.md
- Guides:
- Configuration Support: Guides/Configuration.md
- Variables: Guides/Variables.md
- Parallel Tasks: Guides/ParallelTasks.md
- Branch Variables: Guides/BranchVariables.md
- Extension Syntax: Guides/ExtensionSyntax.md
- Logging: Guides/Logging.md
- Modules: Guides/Modules.md
- Notifications: Guides/Notifications.md
- Working with Genomic Regions: Guides/Regions.md
- Reports: Guides/Reports.md
- Resource Managers: Guides/ResourceManagers.md
- Tool Version Database: Guides/ToolVersionDatabase.md
- Trash: Guides/Trash.md
- Development Setup: Guides/DevelopmentSetup.md
- Documentation Style: Guides/DocumentationStyle.md
- Implementing A Resource Manager: Guides/ImplementingAResourceManager.md
- Troubleshooting: Guides/Troubleshooting.md
- Listening for Pipeline Events: Guides/PipelineEvents.md
- Advanced Settings: Guides/AdvancedSettings.md
- Adding to Class Path: Guides/ExtendingClassPath.md
- Pre-allocating Resources for Jobs: Guides/PreallocatedJobs.md
- Integration with Gitlab: Guides/Gitlab.md
- Integration with JMS / Queuing Systems: Guides/JMS.md
- Using Bpipe with Amazon Web Services (AWS/EC2): Guides/AWS.md
- Using Bpipe with Google Cloud (GCS): Guides/GoogleCloud.md
- Running Commands in Containers: Guides/Containers.md
- Examples:
- Paired End Alignment: Examples/PairedEndAlignment.md
- RNA Seq Corset: Examples/RNASeqCorset.md
- WGS Variant Calling: Examples/WGSVariantCalling.md
- Releases:
- 0.9.11 (latest): Releases/0.9.11.md
- 0.9.10: Releases/0.9.10.md
- 0.9.9.9: Releases/0.9.9.9.md
- 0.9.9.8: Releases/0.9.9.8.md
- 0.9.9.7: Releases/0.9.9.7.md
- 0.9.9.6: Releases/0.9.9.6.md
- 0.9.9.5: Releases/0.9.9.5.md
- 0.9.9.4: Releases/0.9.9.4.md
- 0.9.9.3: Releases/0.9.9.3.md