Torsten Seemann

This is quite hard to do in the current framework. You might need to do `vfcallelicprimitives` on each `snps.raw.vcf` then `vcfcombine`, or use some modules in `vt`.

How would you want the JSON arranged? ``` sample: assay1: assay2: ``` or ``` assay: sample1: sample2: ``` etc

The capability to begin with assemblies instead of reads (or mix thereof) is an existing open issue. It might be possible to hack it to work. You would need to...

If you don't have proper paired read files then Nullarbor will fail, as all the tools expect the same number of reads in R1 and R2. I don't check this...

What species is mixed with what species?

Garbage in, garbage out. Megahit would probably do ok with it. Not really a problem I can solve, and yes, Makefiles don't handle this well :(

@kwongj that would be good, but a little tricky because of the makefile architecture. in fact most pipelines struggle with "business logic" in the middle of things. there are a...

@labrat9 You can run `make -k` which "keeps on going" despite any failed sections. `make` itself has no capability to do "business logic". I would need to add in "helper...

Currently it does not support globbing, but it's a good idea. I was considering making `prefill:` a list of paths too, instead of a single one. What would you want...

how many folders do you expect `/*/` will match in your case?