All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
- Arriba v2.4.0 high confidence calls as fusion candidates
- [easyquant] (https://github.com/TRON-Bioinformatics/Easyquant) v0.5.2 for read support requantification
- Unit/integration tests using pytest
- Fixed issue with gene names in fusion annotation script
- Updated prediction model based on new results
- Moved conversion, parsing and annotation code from the easyfuse-src package
- Removed unnecessary columns from final output
2.0.2 - 2023-11-24
- Upgraded pipeline to Ensembl v110
- Updated to FusionCatcher v1.33
2.0.1 - 2023-08-11
- Simplified installation and dependency management through migration of EasyFuse package to Bioconda
- Fixed bug in QC workflow
2.0.0 - 2023-07-07
- EasyFuse as NextFlow pipeline for increased usability, stability, and scalability
- Python code as python package outsourced to separate repository
- Internal detection tools were reduced to StarFusion and FusionCatcher
- Prediction model has been changed to EF_requant_type to not rely on specific tool features
- Overall reduced detection performance in sensitivity and precision compared to EasyFuse 1.3.7
1.3.7 - 2022-12-15
- Updated models and provide additional models for feature subsets
- Cleaned code and made it more robust
- Updated error handling
- Cleaned up Dockerfile and made versioning more strict
- Fixed bugs related to Python compatibility
- Fixed read counts from tools in final results table
1.3.6 - 2022-07-21
- Add support for Singularity
- Update example output files
- Make Dockerfile more flexible
- Update README
1.3.5 - 2022-06-20
- used a breakpoint-specific identifier (BPID) for joined annotation and in output
- new output file names
- separate output files for predicted fusions .pred.csv and all candidates .all.csv
- new output format including column BPID
- retrained model on new output column format
- cleaned up R code and updated R dependencies
- added Docker example scripts with test data and run_test.sh script
- added support for INI and JSON config files and make them more user-friendly
- fixed content of columns _detected, tool_count, and tool_frac
- fixed several bugs in input file/folder parsing
1.3.4 - 2021-05-29
- updated prediction models EF_full (default) and EF_full_rep (with replicates).
- Fixed bug in fastqc parsing from different sources
1.3.3 - 2021-05-29
- Added option to select Fusioncatcher index
- Fixed some bugs for non-queueing environments
1.3.2 - 2021-05-29
- include updated prediction model
- remove the creation of unused files
1.3.1 - 2021-05-29
- Restructured code
- Switched to Python config file as it provides more convenience and better usability
- Fixed some bugs in summarization scripts
- Fixed some bugs when no fusions are found
1.3.0 - 2021-05-21
- Initial release on GitHub