add --aligner to choose between bwa-mem and bwa-mem2

[maxulysse]

Struggling a bit to compute a conda env on my computer, with bwa and bwa-mem2, but also with either one of them.
So finally, opposed to what I said on Slack, I'm trying to have both of them at once, and see if it build on dockerhub.

nf-core/sarek pull request

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[FriederikeHanssen]

Maybe I missed it, but if bwa-mem2 is set for the --aligner, shouldn't then params.bwa=false be set by default, to avoid the indices mess? Or are you going to set them all in igenomes after all?

[maxulysse]

Default would be bwa-mem currently, so no issue with the current indices:

sarek/nextflow.config

Line 43 in c12f9d8

aligner = 'bwa-mem'

[FriederikeHanssen]

OK, but if I set --aligner-bwa-mem2, then I have to set bwa=false, too, right? Maybe this can be already included, if this aligner is chosen?

[maxulysse]

That's a very good point.
I'll add that to the doc right away

[FriederikeHanssen]

The bwa changes look good. can't say much about the json schema. For me it looks good, but I haven't played around with it so far.

[maxulysse]

I know now that the conda env takes around 3 hours to compute, so trying again on my side to see if it all works well.
Hopefully can merge that today