Changelog

### Added
- Added  new flag `--removecontam` to the report command to remove contaminants from the reports
- Added a new combined_psm report to abacus (beta)


### Changed
- Updated the TMT-Integrator to match with the version v4.0.0
- Updated the pickedFDR filter
- The pipeline command now accepts annotation files with prefixes
- Updated PTMProphet to the latest release
- Updated the database fetch with the new UniProt API (The new API is still unstable, people might experience hicups with certain cases, specially non-model organisms without reviewed sequences)


### Fixed
- Contaminant tags are now added to Human sequences as well
- Several minor fixes and updates
- Added a fix to fix errorrs causes by division-by-zero errors (PR by @chhh)
- Fixed the protein coverage calculations to take into account all peptides