To run dada2 denoise-ccs, you currently have to specify a --p-front which would generally be your FW primer. I assume that the main reason that this flag is required, is to re-orient the reads in the same direction, as PacBio results in mixed orientations.
However, as discussed in this post and in some others, if you first extract the ITS regions using itsxpress you lose the primer primer regions and thus cannot use dada2 denoise-ccs anymore because it is not possible to specify a --p-front.
Hence, I think it would be very valuable if dada2 denoise-ccs could be run on pre-oriented PacBio reads without the --p-front parameter. There could for example be implemented using a boolean flag like --reads-orientedwhich you can label as TRUE or FALSE to input if the reads are already oriented or not. If TRUE, denoise-ccs can be run without --p-front. If FALSE, a --p-frontsequence is required.
Perhaps I'm missing something and this is not possible.