Just one note, some time ago I created [this shared module](https://nf-co.re/modules/custom_gtffilter/) for filtering the GTF based on FASTA. Maybe it is useful for scrnaseq _Originally posted by @nictru in https://github.com/nf-core/scrnaseq/pull/464#pullrequestreview-2789928144_