Added #267 Support for brukers tdf format by adding tdf2mzml converter #269 DeepLC retention time prediction (shout out to @steffenlem) #270 MS2PIP peak intensity prediction (shout out to @steffenlem) #271 Added OpenMS FileFilter to clean mzml after parsing to remove artifacts like empty spectra or precursors with charge 0 (optional) Made file extension check case insensitive Added option to provide a default comet parameters file @steffenlem #273 Optimize resource allocations https://github.com/nf-core/mhcquant/pull/274 Template update 2.9 #280 Improved quantification such that merged FDR-filtered runs can be quantified properly https://github.com/nf-core/mhcquant/pull/282 Template update 2.10 Fixed https://github.com/nf-core/mhcquant/pull/266 New OpenMS version 3.0.0 fixes duplicated ID bug https://github.com/nf-core/mhcquant/issues/250 Dependencies #266 Switched from OpenMS version 2.8.0 to newest version 3.0.0 #266 Bumped ThermoRawFileParser version from 1.4.0 to 1.4.2 Deprecated #280 OpenMS RT prediction