Hi. I am having some doubts about what the % endogenous from endorspy means. From looking at the log, it seems that endorspy is run before removing duplicates. Is this correct, and if so, is there a way to run endorspy only after removing duplicates?

Hi Gonçalo! Endogenous DNA % usually refers to the proportion of the sequenced material that is human. Hence it is ran before deduplication, since that would artificially lower the estimate and change its definition. Since sometimes the calculation can be usedul to do after quality filtering, eager will provide an additional 'post-filtering' estimate of enogenous if filtering is done. The fraction of unique quality filtered reads / total reads is not something that is calculated by eager. That said, you can calculate the fraction of unique reads easily from the MultiQC general stats table, since both those numbers are provided

I think(?) we described this also in the output docs: https://nf-co.re/eager/2.5.3/docs/output/