Hi @Kata Ferenc! Merry Christmas! I've made a PR to our nf-core dev after making sure that the full pipeline runs with default params and with some alternative params (see the list of tests that I'm following here: https://github.com/ComputationalRegulatoryGenomicsICL/cageflow/issues/32). Could you please have a look when you have time and merge if it looks OK? -- https://github.com/nf-core/cageseq/pull/86 I'll return to the testing and fixing in a couple weeks and will address the issue of not providing a genome FASTA file (I will rebuild the schema and make sure that the parameter is automatically checked as mandatory).