I know I've seen this information somewhere but for the life of me I can't find how to pass command line options to variant callers. I want to use --disableEVS for Strelka. I am using sarek 3.6.0 which I know is old at this point but that was the version originally used on these samples.

you should be able to do this via ext.args in a custom config file

Thank you for your reply. In the linked article there is a warning that "The numeric order of

args

keys must match the order of tools as they appear in the module script." Does this mean I need to be mindful of what I number my args if I am using multiple variant callers at a time?

no, that should not matter much, I think this was more for process with multiple tools, that have args, arg2 and so on. What I would pay attention instead, is checking what are the ext.args sarek is setting up from strelka and be careful of including all of them in your new config file on top of disableEVS otherwise you will have some surprises in the results

How do I check the ext.args that sarek is setting up?

Here: github.com/nf-core/sarek/blob/…/strelka.config

Thanks @Famke Bäuerle I missed this message