Major changes

Added a model for epitopes
Optionally, output a table with all annotated epitopes obtained from a set of input neoantigens (option --with-all-neoepitopes)
Additional command line tool neofox-epitope that accepts epitopes as input. The epitopes may be associated with a particular HLA allele or alternatively paired with each of the HLA alleles defined in a given patient
MHC-II weak binder threshold changed from 10 to 5
Output JSON file with reference resources metadata with the aim of documenting the reference data versions

Minor changes

Neoantigen model is simplified by removing the Mutation entity
Annotations are renamed with the aim of making them more self explanatory
Always output tabular and JSON data as opposed to choosing output format
Input parameters --candidate-file and --json-file are simplified into --input-file. The format of the input is inferred from the file - extension, being valid extensions *.txt and *.tsv for tabular format; and *.json for JSON format.
Recognition potential is now also annotated when mutation not in anchor positions
Dask cluster is now closed in a cleaner way
Some of the binaries are now optionally read from the PATH
All temporary files from MHC prediction are removed now, this caused troubles for large datasets
Now all relevant peptides of length 8-14 are considerd while MHC-I prediction (previously: 8-11)