One anxiety I have regarding this pipeline is that

ribotricer

is the primary method for detecting translated open reading frames. Inclusion of a tool in a nf-core pipeline has an element of endorsement to it and ribotricer is known to be one of the least reliable callers out there. I believe it was included as it was reliably installable and run-able. Admittedly there is no consensus on what should be used instead but perhaps we should be doing more to communicate just how unsolved this problem is

That's a valid concern—usability often outweighs performance in popularity, even when more robust tools exist. Including multiple tools could dilute perceived endorsement, and clear documentation can help communicate the field's limitations until we include more. Another approach could be reaching out to developers of promising tools, letting them know we’re considering including their tool in a gold-standard ribo-seq pipeline and inviting them to collaborate on improving usability. At the end of the day, developers who want their tools widely adopted should prioritise making installation and use as simple as possible.

Unfortunately, with 'standard' pipelines, the 'runnability' and maintenance status have to be quite close to the top of priority lists. Clearly I have not object to replacing ribotricer with a better tool that meets those criteria!

@Jack Tierney what would be a couple of tools you have in mind?