parameterize number of cores in main.nf

[nhoffman]

COU allocation is hard-coded for cmsearch and vsearch - either add parameters for these in the profile, or use as many are available within the task.

[dhoogest]

Scott pointed this out today as well when reviewing load on agrajag (I was running some NGS16S dev analysis there). Vsearch step took all available cores, which for that machine is a lot : )

[crosenth]

How does this look? 594c6ec

[dhoogest]

Looks fine to me as a simple solution!

[dhoogest]

Does cmsearch also allow for ncores specification? Sounds like that step is also greedy

[crosenth]

Yes here or is it not working? https://github.com/nhoffman/dada2-nf/blob/master/main.nf#L180

[crosenth]

Not sure what profile you using but queueSize should also be set to a reasonable number:

https://github.com/nhoffman/dada2-nf/blob/master/nextflow.config#L48