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Conference season abstracts are due soon (GCC and ISMB/BOSC). I (@jmchilton) would like to follow up last year's talk "Planemo – A Galaxy Tool SDK" with a talk "Planemo – A Scientific Workflow SDK" suitable for both BOSC and GCC.
Talk Outline:
- Overview of Recent Galaxy Workflow Enhancements:
- Implicit connections.
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Backend galaxyproject/galaxy@e0a5e82 - UI (TODO)
- Slide
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- Nested Workflows.
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First pass in 16.01. New Workflow Modules - Input Parameters and Subworkflows galaxy#1306 - Follow up - allow "upgrading" workflows.
- Slides
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- Labels on all the things.
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Implementation New Workflow Modules - Input Parameters and Subworkflows galaxy#1306 - Slide
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- Collection Operations and Patterns.
- Implementation (Issue Collection Operations galaxy#1644, Failed PR Collection Operations galaxy#1313) New PR (Collection Operations (Limited) galaxy#2434)
- Slides
- UI enhancements.
- Slide
- Implicit connections.
- Format 2 Galaxy Workflows - A writable specification for native Galaxy workflows.
- Implement population of default tool state (TODO: create Galaxy issue and PR)
- Better handling of conditionals (Simplify required conditional spec. in .ga workflows. galaxy#1777)
- Describe format, give examples.
- Slides
- Implement a library on top of bioblend. https://github.com/jmchilton/gxformat2
- Usage.
- Serving Workflows
- Profiles for workflow development. Galaxy Profiles for Planemo #445.
- Serve for Galaxy workflows (
planemo serve <workflow>). ImplementEngineandRunnableabstractions. #454 - Enhanced profiles for Galaxy. Improved Galaxy Profiles #447.
- Slides
- Running Workflows (
planemo run <workflow> <job>)- Initial engine implementation Implement
EngineandRunnableabstractions. #454 - Refine engine for workflows
- Slides
- Initial engine implementation Implement
- Testing Workflows (
planemo test <workflow>)- Pull Galaxy test stuff out into galaxy-lib for reuse here.
- Refine engine for testing.
- Slides
- Serving Workflows
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The State of the CWL (skip at BOSC)(@mr-c submitted an abstract - will cover this).-
Slides (Michael and Peter will probably have something to use there).
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- Building and Testing CWL Tools with Planemo
- Build and lint. (Infrastructure and docs for building and linting CWL tools #466)
- Test with cwltool.
- Test with Galaxy.
- Serve in Galaxy.
- Building and Testing CWL Workflows with Planemo
- Lint and test with cwltool.
- Future plans - Galaxy support.
- Planemo Machine - An Environment for Galaxy and CWL workflow development.
Too Stretched Goals:
- Workflows from file paths like tools (Instance (user-less) Workflows galaxy#1740)
Remaining dev priorities:
- Emphemaris and shed picture for gxformat2 workflows!
- Implement
--slurm.
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