Hey @Leendert Cloete you are in the correct place. Using the

--genome

parameter you specify the pipeline to use iGenomes. You should read this before you move on. In the beginning of the pipeline, it filters out all GTF entries that are located on sequences that do not exist in the FASTA file. This is most likely because the chromosomes are annotated differently. Moving forward I suggest you to download your genome GTF and FASTA from a source of your choice, e.g. here. All the tool indices will be generated if you don't provide them, so no need to worry. If you want to re- use them in future runs, you can use the

save_reference

parameter, copy them from the pipeline output dir to a permanent location and reference them from there. Let me know if you have any other question!