nfcore/quantms v1.2.0 - Thimphu

Added Feature

• #275 BigBio Added support for bruker data in DIA branch @daichengxin @ypriverol @jspaezp.
• #275 BigBio And speed-up to DIA-NN pipeline @jspaezp.
• #275 BigBio Support for library-base search in DIA-NN pipeline @jspaezp.
• #300 BigBio Major refactoring of LFQ-DDA MBR algorithm @jpfeuffer @ypriverol @timosachsenberg.
• #279 BigBio Support for SAGE search engine @jpfeuffer @timosachsenberg @ypriverol.
• #122 BigBio Update openms 3.1.0 by @ypriverol @timosachsenberg

Changed

• #314 Update for pmultiqc to pmultiqc=0.0.23 @WangHong007 @daichengxin
• #308 Update for openms to openms=3.1.0
• Update for sdrf-pipelines to sdrf-pipelines=0.0.24
• Update for msstats to msstats=4.2.1

Fixed

• #316 Fixed jar path selection of luciphoradapter and msgf+
• Fixed bug where modification masses were not calculated correctly in DIA-NN conversion.
• Fixed multiple bugs Pull Request #293 BigBio, #279 BigBio, #265 BigBio, #260 BigBio, #257 BigBio

### Additional changes

• Post 1.1.1 release workup by @fabianegli in #100
• Merging template update 2.9 by @jpfeuffer in #108
• Important! Template update for nf-core/tools v2.9 by @nf-core-bot in #103
• Update diann_convert.py by @daichengxin in #121
• Minor changes by @ypriverol in #124
• Multiple changes before the release. by @ypriverol in #125
• Use https instead of http for shields.io resources by @fabianegli in #126
• Mypy found issue fixes by @fabianegli in #127
• More fixes for type annotations by @fabianegli in #128
• More fixes for type annotations by @fabianegli in #129
• set release date and release version by @fabianegli in #131
• Version 1.2 [PLEASE DO NOT MERGE YET] by @ypriverol in #120

Full Changelog: 1.1.1...1.2.0