2.0.3

Added

• Arriba v2.4.0 high confidence calls as fusion candidates
• easyquant v0.5.2 for read support requantification
• Unit/integration tests using pytest

Changed

• 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

• Upgraded pipeline to Ensembl v110
• Updated to FusionCatcher v1.33

2.0.1

• Simplified installation and dependency management through migration of EasyFuse package to Bioconda
• Fixed bug in QC workflow

2.0.0

This release includes the following major changes:

• 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

• Fixed bugs related to Python compatibility
• Fixed read counts from tools in final results table
• 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

1.3.6

• Add support for Singularity
• Update example output files
• Make Dockerfile more flexible
• Update README

1.3.5

• used a breakpoint-specific identifier (BPID) for joined annotation and in output
• output changes:
  • new output file names
  • separate output files for predicted fusions .pred.csv and all candidates .all.csv
  • new output format including column BPID
  • fixed content of columns <tool>_detected, tool_count, and tool_frac
• 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 several bugs in input file/folder parsing

1.3.4

• updated prediction models EF_full (default) and EF_full_rep (with replicates).
• Fixed bug in fastqc parsing from different sources

1.3.3

• Fixed some bugs for non-queueing environments
• Added option to select Fusioncatcher index

1.3.2

• include updated prediction model
• remove the creation of unused files