I see that @mashehu updated the cageseq dev branch with our branch from last week. Since then we did some fixes as discussed, but now the pipeline crashes ( we needed to replace getchromsizes with samtools/faidx and that broke something we dont understand), so would be nice to get some support. @Slava Sidorov and myself actually get two different looking errors probably because i am using a bit older nextflow version, so that's also something to figure out