all(samples$sample_id %in% colnames(counts)) is not TRUE

. I suspect this has something to do with R messing with column names (by default), where it replaces dashes,

+

, etc., with periods. I had a lot of issues getting the pipeline to run through all of the tools, because each had different issues with names (e.g. dashes are used to separate comparisons in some, so if you already have them in samples it get borked. Keep it as simple as you can. 🤞