This release utilizes the v.2024-12-05 version of the underlying database and contains changes from several pull requests: #27, #28, #29, #30, #31.
Additions:
- A new output of the suffix .input-metadata.txt. This converts the patients dictionary, which contains input details such as string label, tumor purity, ploidy, and msi status, into a dataframe and outputs it as a table. From #30 .
- A new output of the suffix .moalmanac-execution.json. This compiles all config settings set in config.ini, execution runtime, input file paths, input datasource paths, input metadata, as well as each tabular output into a single json file. From #30 .
- A new script
moalmanac/run_4x_for_output_regression_test.pyto run themoalmanac/run_example.pyfour times using different config settings and with and without input files. From #29.
Revisions:
moalmanac/logger.pywas revised to shut down at the end of moalmanac's main function, allowing for multiple processes to be executed in series within a single Python process. From #29.- Annotating with ExAC, ExACExtended, and ClinVar will now skip rows that have missing data in any of the required columns. From #28.
- Docker now uses Python 3.12 and also pushes to the
latesttag. From #27.
Bug fixes:
- Columns with empty values within read count columns would cause the process to fail. From #28.