Changelogs » Dahak-taco

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Dahak-taco

1.0beta

Added
  
  - Revamped documentation
  
  - Added unit tests (run with nose, or nose collector via setup.py)
  - tests for success (uses taco-simple workflow repository)
  - tests for failure (incorrect usage)
  
  - Tests can be run with `python setup.py test`
  
  Removed
  
  - `goodies/` - not used, see [taco-simple](https://github.com/dahak-metagenomics/taco-simple)

0.3

Changed
  
  - Abstraction for taco has been updated to facilitate testing.
  We are now separating the workflow details from taco itself.
  
  - taco utility is now a command line tool, installed with setup.py
  
  - Workflows should now exist locally, taco anticipates a particular
  directory structure and will raise exceptions if things aren't
  in place
  
  - This structure becomes more logical when we think about the
  alternative: bundling everything together requries dealing with
  in-memory Snakefiles, creating a temporary folder on disk to
  extract and run, etc. Yikes.
  
  Removed
  
  - Standalone taco script
  
  - Docker files (moved to workflow repositories)
  
  - Rule files (moved to workflow repositories)
  
  Fixed
  
  - Add setup.py to make this a pip-installable,
  semantically-versioned, testable, cross-platform
  package.
  - Update the command line interface syntax to handle
  verbs and command line options in a more logical fashion.

0.2

Added
  
  - Revisiting read filtering to fix parameters
  - Added tests (for now, dry runs)
  
  Fixed

0.1

Added
  
  - Completed read filtering workflow
  - Added ability to use custom Dockerfile
  - Previous work: implementing rules files for read filtering,
  implementing taco command line, adding documentation, etc.
  
  Changed
  
  - Added `use_local` parameter (boolean: use a local docker image?)
  - Added `local` parameter (name of local docker image to use)
  
  [List of Change Categories]
  
  Added
  
  Changed
  
  Deprecated
  
  Removed
  
  Fixed