Hello everyone! I would like to support a way to improve this pipeline. First of all, I would like to thank all contributors as well as the people who originally created this pipeline, because it provides a great starting point for de-novo transcriptome assembly. Currently, this pipeline arrives at an assembled transcriptome that doesn't have particularly helpful annotations, since Trinity gives its own IDs to transcripts that don't look like the known ones. The missing step is to annotate these transcripts (e.g. with BRAKER3 or Augustus), make predictions for Gene Ontology associations, find protein sequences, protein domains etc. Such a single pipeline does not exist in nf-core, but it does exist in Snakemake (eg., https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13593 and https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05254-8). It is not necessarily novel in the sense that no one else has thought of it, but the fact remains that it does not exist in nf-core. We could possibly add other best-practices to the analysis, such as PCR artifact deduplication, or even giving reference organisms and finding homologs to make a very comprehensive pipeline. There is also this paper on the steps of de-novo transcriptome assembly. https://academic.oup.com/bib/article/23/2/bbab563/6514404 It would be my pleasure to contribute to this task and improve this current implementation. I believe it would be helpful for a lot of scientists especially now since there is a mass sequencing of new genomes.