Can someone help me understand the vep_plugin_files parameter? I am confused on exactly what I am suppose to provide. I have the plugins installed in the same directory as the vep_cache. I am not sure what databases or tools to use for the recommended plugins: LofTool, pLI,SpliceAI, and MaxentScan

spliceAI you need to login and download from Illumina's site (base-space I think). pLI_values and LoFtool_scores, I copied manually from the test dataset I think..I think https://github.com/nf-core/test-datasets/tree/raredisease/reference be careful some files are subset to chr20 ... but not these in question MaxEntScan I didn't need anything I don't think...

Hi! i just downloaded them from here: wget https://github.com/Ensembl/VEP_plugins/archive/refs/heads/release/115.zip unzip 115.zip hope it is still useful!

Hello I downloaded the plugins but I was wondering if I needed the MaxEntScan matrices. It doesnt look like it was used in the test run so Benjamin might be right but I just want to make sure