A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Is there a parameter set how I can run the pipeline to only do SV Benchmarking?

as in a route through the benchmarking tools - or do I just only set SV related stuff in my parameters then?

It is a bit messy now but if you set sv truth and select sv benchmark tools (truvari and svbenchmark ) it should work through only sv benchmark. I would be happy to do the setup with you if you need help.. at the hackathon I discovered it is not easy for the users now :sweat_smile: :face_holding_back_tears: :face_holding_back_tears: promise it will be better soon 

Hello Famke, I seperated SV and small variant calling more clean. If you wanna try it out I have two test cases: <https://github.com/nf-core/variantbenchmarking/blob/121-more-clean-bcftools-normalizations/conf/tests/germline_sv.config> and <https://github.com/nf-core/variantbenchmarking/blob/121-more-clean-bcftools-normalizations/conf/tests/somatic_sv.config> please let me know if you need more help