--mirtrace_protocol arguments redundant, --protocol only should be sufficient

[gpalidwor]

Description of feature

Currently smrna requires both --protocol and --mirtrace_protocol to be set. Both default to illumina. If --protocol is set to a non illumina value (e.g. nextflex) --mirtrace_protocol must be set to the same. As such the --mirtrace_protocol argument is redundant and can lead to confusing results if not set to match --protocol. I can think of no cases where --protocol and --mirtrace_protocol should be different

[apeltzer]

So when I have a look at the code, it has a flag that sets mirtrace_protocol to params.protocol whenever mirtrace_protocol has not been set.

[gpalidwor]

Thanks for looking at it; My experience was the mirTrace output was not meaningful (didn't map to anything) for --protocol nextflex until I also set --mirtrace_protocol nextflex so perhaps it's protocol specific..?

[apeltzer]

Fixed in dev