Hello everyone! I noticed that in version 2.11.0 of Ampliseq, there is a READ-THROUGH module for sample pre-processing. I have been searching but can not find any option to enable this process with CUTADAPT. Is there a way to activate it through the config or is it done via other flags? Thank you very much in advance, and congratulations on the program!

Hi, this is activated by https://nf-co.re/ampliseq/2.11.0/parameters/#illumina_pe_its I agree thats a little hidden and doesnt serve the purpose exactely, because read truncation will be disabled as well if you do not actively set

--trunclenf

and

--trunclenr

Thank you so much for the quick answer!