Hi everyone, I know you can run the nf-rnaseq pipeline with custom organisms and annotations; is there a way i can provide a custom gff file for rnasplice? It's still on the TAIR10 genome but the (splicing) annotation on ensemble is quite outdated so i would like to use my own. I couldn't find anywhere how to do it. I am sorry if i missed it.

Use of iGenomes for rnaseq and rnasplice is not recommended (because of the age of the gene annotation and other issues), and you only need two files, a genome FASTA and a GTF/GFF, which you specify via

--fasta

and

--gtf

(or

--gff

, but note that any GFF will be automatically converted to GTF, so if you have a GTF, it would be more efficient and less error prone). Just be sure that the GTF/GFF and the FASTA are compatible (same contig names, same assembly). (You can save any derived reference files [e.g. the STAR index] and supply them via parameters to subsequent runs, which would be more efficient.)

Thank you so much!