Dear all can I use config file as in sarek with -c option in scrnaseq? Thanks in advance.

of course

Can you clarify what you're trying to achieve? The configuration for sarek is specific to Sarek. Nf-core also has institutional profiles which configure all pipelines to run on a specific infrastructure ( which I guess is more what you're looking for ). If you search nf-core/configs https://nf-co.re/configs/ to see if you have a institute specific profile, you can use that to run Sarek, or scrnaseq, or any other nf-core pipeline on your infrastructure

-c

is a nextflow option, so that'll work with any Nextflow pipeline

I want to control how much resources to use for different processes and where too save the intermediate files and so on.

then basic configs as in the config repo should work without issue