GATK4 dependencies

[matthdsm]

Hi!
I wanted to open a meta issue to consolidate all the efforts to actually get GATK4 to work (completely) through bioconda.

So far I've found draft PR's by
@mjsteinbaugh
@jmarshall
@ryanjameskennedy

Is there some kind of roadmap on which we can work together, so we don't duplicate any efforts?

I particularly liked @jmarshall 's idea to create a gatk-slim package, similar to picard, in #41127

GATK references an environment file in its installation docs, found here. This contains a set of (ancient) dependencies, which are needed to get the GATK python scrips to work.

I would suggest we try to replicate this set of dependencies?

Any and all thoughts are welcome!

Also pinging in @nvnieuwk and @maxulysse to get the nf-core folks in the loop

[matthdsm]

There seems to be some ongoing work upstream
broadinstitute/gatk#8561, but it's not been active for a couple of months

[maxulysse]

Nice investigation <3

[matthdsm]

Attempt in #45759

[matthdsm]

#45762