3.0.0 - Wanne - 2025-05-09

#279 - Add SUMMARIZE_RESULTS module and MultiQC plots. BREAKING output structure change from<outdir>/predictions/<meta.id>/<meta.id>.tsv to <outdir>/predictions/<meta.id>.tsv
#270 Added option --wide_format_output to provide wide format output with additional information instead of long format (default)

#247 - Update to nf-core template 3.0.2
#255 - Update to nf-core template 3.1.2
#250 - Implemented netmhcpan module. Removed legacy netmhc tools. Only the latest netmhcpan and netmhciipan versions will be supported (netmhcpan-4.1b, netmhciipan-4.3e)
#252 - Implemented netmhciipan module
#253 - Implemented mhcflurry module
#259 - Implemented mhcnuggets and mhcnuggetsii module
#260, #270 - Major refactoring to new, modular MHC binding subworkflow (see Meta-Issue #205). Removed legacy predictor syfpeithi. Predictors that can be specified via --tools are: mhcflurry,mhcnuggets(default),mhcnuggetsii,netmhcpan,netmhciipan. Changed --min_peptide_length and max_peptide_length to min_peptide_length_classI and --max_peptide_length_classI.
#263 - Rearrange supported alleles per predictor
#266, #268 - Refactor variant prediction with epytope
#282 - Update to nf-core template 3.2.1

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