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.
    • Backend galaxyproject/galaxy@e0a5e82
    • UI (TODO)
    • Slide
  • Nested Workflows.
    • First pass in 16.01. New Workflow Modules - Input Parameters and Subworkflows galaxy#1306
    • Follow up - allow "upgrading" workflows.
    • Slides
  • Labels on all the things.
    • Implementation New Workflow Modules - Input Parameters and Subworkflows galaxy#1306
    • Slide
  • 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
• 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>). Implement Engine and Runnable abstractions. #454
      • Enhanced profiles for Galaxy. Improved Galaxy Profiles #447.
      • Slides
    • Running Workflows (planemo run <workflow> <job>)
      • Initial engine implementation Implement Engine and Runnable abstractions. #454
      • Refine engine for workflows
      • Slides
    • Testing Workflows (planemo test <workflow>)
      • Pull Galaxy test stuff out into galaxy-lib for reuse here.
      • Refine engine for testing.
      • Slides
• 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).
• 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.