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Galaxy Workflow Format 2 Descriptions

Project description

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This package defines a high-level Galaxy workflow description termed “Format 2”. At this point, these workflows are defined entirely client side and transcoded into traditional (or Format 1?) Galaxy workflows.

The traditional Galaxy workflow description is not meant to be concise and is neither readily human readable or human writable. Format 2 addresses all three of these limitations.

Format 2 workflow is a highly experimental format and will change rapidly in potentially backward incompatible ways until the code is merged into the Galaxy server and enabled by default.

History

0.10.1 (2019-12-07)

  • Bug fix to handle outputs without labels in Format 2 - they don’t validate per se but they are important for testing in the Galaxy framework.

0.10.0 (2019-12-06)

  • Implement scheam, validation, linting (for Format 2 and .ga).
  • Handle new reports field in Galaxy 19.09 workflows.
  • Numerous fixes for conversiion to and from native workflows.
  • Numerous new test cases.
  • Implement Java project for valiating and linting both kinds of workflows.

0.9.0 (2019-07-08)

  • Implement default values in gxformat2.

0.8.4 (2019-06-24)

  • Fix output IDs of 0.

0.8.3 (2019-05-23)

  • Implement set_columns PJA.

0.8.2 (2019-03-16)

  • Allow another API return option for experimental tool creation API.

0.8.1 (2019-03-11)

  • Implement change datatype PJA.

0.8.0 (2018-11-01)

  • Implement experimental CWL-style step defaults (see Galaxy PR #6850).

0.7.1 (2018-10-09)

  • Various small fixes for changes in 0.7.1.

0.7.0 (2018-10-08)

  • Add some basic test cases.
  • Allow ID-map style listing of steps.
  • Ordered load (in addition to existing dump functionality) or ordering of steps in ID-map style variant works.
  • Allow CWL-style $graph defs that can define multiple workflows in a single file.
  • Initial work on de-duplicating subworkflow definitions on import.
  • Fix position handling while exporting workflow.

0.6.1 (2018-10-01)

  • Fix export of non-data parameters and implicit workflow connections.

0.6.0 (2018-10-01)

  • Various fixes, allow id map style workflow input definitions.

0.5.0 (2018-10-01)

  • More fixes for PJA, add the doc keyword to format 2 workflows to match CWL workflows. Map to and from native Galaxy workflows as annotations.

0.4.0 (2018-10-01)

  • Fixes for exporting PJA when exporting workflows from native .ga to format 2.

0.3.2 (2018-10-01)

  • Fixes for exporting workflow outputs from native .ga to format 2, support for modern map style output definitions like CWL 1.0.

0.3.1 (2018-10-01)

  • Fixes for exporting subworkflows from native .ga to format 2.

0.3.0 (2018-09-30)

  • More cwl style inputs, initial work on conversion from native workflows, various small fixes and tweaks.

0.2.0 (2018-02-21)

  • Bring in latest Galaxy updates - Python 3 fixes, safe YAML usage, and more PJA implemented.

0.1.1 (2016-08-15)

  • Fix one Python 3 incompatibility.

0.1.0 (2016-05-02)

  • Initial version - code from Galaxy’s test framework with changes based on planemo testing.

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