make trimming adaptor sequence configurable, maybe skip TrimGalore

[steffenheyne]

see dicussion here:
#53

[dpryan79]

An alternative would be fastp. Apparently it's multithreaded and can do a bunch of nice things like filtering by complexity and poly-A content. Some of the Galaxy tutorials might get switched over to this.

[dpryan79]

In case anyone external to us is wondering, I've benchmarked fastp and it's slower than cutadapt once you start using more than ~5 cores. I really like some of its options, so I'm currently trying to figure out if I can speed it up a bit.

[mictadlo]

What about afterqc?

[dpryan79]

@mictadlo My understanding is that afterqc is quite similar, only slower. It's from the same authors and they mention that in the fastp preprint at least. I have to admit to not having tried afterqc, though. If you've found it to be performant and the results to be good then let me know :)

[mictadlo]

Thank you for pointing it out to me. fastp sounds good actually.