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Galaxy Workflow Format 2 Descriptions

Project description

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Format 2

This package defines a high-level Galaxy workflow description termed “Format 2”. The current schema version is v19_09 and the schema can be found [here](http://galaxyproject.github.io/gxformat2/v19_09.html). This version of workflow format can be consumed by Galaxy versions 19.09, 20.01, 20.05 and the the forthcoming 20.09.

The Format 2 workflow description is still somewhat experimental and may yet change in small potentially backward incompatible ways until the format is exported by Galaxy by default.

The traditional Galaxy workflow description (files ending in .ga extension sometimes called native workflows in this project) was not designed to be concise and is neither readily human readable or human writable. Galaxy workflow Format 2 is being designed to addresses all three of these limitations. While also moving Galaxy’s workflow description language toward standards such as the Common Workflow Language.

gxformat2

This Python project can be installed from PyPI using pip.

$ pip install gxformat2

Checkout the project tests or how it used in projects such as Planemo and Galaxy to see how to use the gxformat2 library. Reference documentation for the modules can be found as part of the project’s documentation.

This project also includes various scripts for working with Galaxy workflows. Checkout their help for more information.

$ gxwf-lint --help
$ gxwf-viz --help
$ gxwf-abstract-export --help

This library and associated scripts are licensed under the Academic Free License version 3.0.

History

0.15.0 (2020-08-12)

  • Lint types of default values.
  • Fix bugs in schema related to differing type names between Galaxy and CWL.
  • Generate cwl v1.2 instead of cwl v1.2.0-dev5 release now that it has been released.
  • More testing of linting and CWL 1.2 export.

0.14.0 (2020-08-11)

  • Bug fix where native export had explicit outputs declaration still in it (wouldn’t break anything, but was deceptive).
  • Fixes for experimental CWL 1.2 abstract export.
  • Improve script structures and documentation.
  • Improve code structure - add more types, make more things immutable, mention mutability in docstrings.

0.13.1 (2020-08-03)

  • Improve package structure - publish fixed sphinx docs, fix readme badges, add mypy typing support.

0.13.0 (2020-07-30)

  • Add experimental export to CWL 1.2 using new abstract Operation classes.

0.12.0 (2020-07-27)

  • Drop support for Python 2 - to support next bullet.
  • Update schema parser for recent changes to schema salad.

0.11.4 (2020-07-27)

  • Added abstraction for uniform access to workflow outputs across formats.

0.11.3 (2020-07-23)

  • Bug fixes for exporting newer input concepts from native to Format 2.
  • Added abstraction for uniform access to workflow inputs across formats.

0.11.2 (2020-07-22)

  • Rework cytoscape and helpers for reuse from Planemo.
  • Rev markdown validator for and from latest Galaxy changes.

0.11.1 (2020-02-25)

  • Bug fix for gxwf-lint invocation from setup.py installed script.

0.11.0 (2020-02-25)

  • Validate Galaxy Markdown in workflow reports as part of linting.
  • Improved null handling in native ga workflow linting.
  • Enhancements to workflow linting from Python. Lint for lack of documentation, tools using the test toolshed, and implement special linting for training material workflows to ensure a tag matches the workflow topic.
  • Add gxwf-viz script that produces a cytoscape visualization of a workflow.

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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