New features

A list of transcription factors was added for all the supported species
The user can now specify the output directory by modifying the outputDir parameter
After a successful run, a log file is generated in the output directory, summarising statistics on the input dataset(s), information on the provided input files and parameters, as well as intermediary results in the workflow
Gene aliases file made optional
Output figures are also generated in PNG format
Ranked regulons file is also generated in TSV format

Improvements and bug fixes

Arabidopsis GO files regenerated to include high-throughput evidence codes
GO files regenerated to exclude duplicated entries
Improved verification of the input files and parameters
Improved the layout of the config file + added more comments
Improved the layout of the output figures
Number of CPUs specified for the GRNBoost2 procedure is now correctly taken into account
Corrected enrichment algorithm that was not always using the correct background size
Corrected file extensions for input and output tab delimited files
Where possible, TF information is extracted from TF list file instead of TF2fam2mot file, removing the need for this file when running MINI-EX without the motif enrichment step
Minor bug fixes

Full Changelog: v2.1...v2.2