I’m new to RNA sequencing and I’m working with non-model, single-celled, photosynthetic eukaryotes. I want to use the nf-core RNAseq pipeline to get transcript abundance but I’m wondering if there is anything I should know about working with the RNAseq pipeline that might make it not the right pipeline to use (I don’t know if it is biased for Human or multicellular organism experiments). Are there parameters for alternative splicing I should be aware of modifying and also is this pipeline still recommended if the organism I’m working with has a sub-optimal genome annotation?

There's nothing scientifically speaking that should limit the workflow to model organisms, in theory it should work with anything with a genome and annotation. I'm guessing high-ploidy plant genomes might require specialist analysis difficult to do here (someone planty might confirm), but that's the only thing that springs immediately to mind. The only thing is the formatting of e.g. GTF files can be a problem. There are a few embedded assumptions about conventions in these files, which come from folks used to dealing with Ensembl and the like, if if those are a bit sketchy you might encounter some procedural difficulties. Really, it's probably easiest to just try some data, see if it gets through, and if it does if the answers make sense with what you know about the biology.

The difference will be the quality of the gene annotation (GTF file) you can get, and possibly the assembly, but these have nothing to do with the suitability of the pipeline per se (it would be an issue with any analysis method). Lack of good annotation would limit the downstream analysis, like pathway analyses, etc. (because you need annotated pathways), but that is outside this pipeline.