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