Major changes include
- Recommended download of reference with
aws --no-sign-request s3 sync s3://nf-core-awsmegatests/rnafusion/references/ <path_to_references> - Changed reference fasta file to the primary assembly, moved from ensembl 102 to gencode 46
- New option to avoid using COSMIC
--no_cosmic - New option to skip generating the VCF summary:
--skip_vcf - New tool: CTAT-Splicing to detect cancer splicing events
- Introduced support to start from CRAM/BAM files and (splice) junctions files
- Fusion-report score is now called the fusion indication index (FII)
- Extra trimming for FusionCatcher in case reads are larger than 100 bp
- Single alignment for arriba and STAR-Fusion
- Use of a parameter
--tools STRINGto select which tools to enable