Hi, when runnig sarek from fastq (--step mapping), is the trimming done by default? In the docs, it is quite confusing: FastP does detection by default, but --trim_fastq is boolean. When I check params.json from my run I can see there is "trim_fastq": false by default.. But when checking FastP docs, it should do trimming automatically...So I don't know Thanks for your help!

yes you need to explicitely enable trimming in sarek by setting

--trim_fastq

. By default a flag is passed to fastp to disable it: https://github.com/nf-core/sarek/blob/4bd2948f98c5bf7b785c91cf6708fffccab25467/conf/modules/trimming.config#L20

thank you