Update GATK4 recipe to allow Java 11 (Proposal)

[jfy133]

GATK4 has had 'beta' support for Java 11 for almost a year now (since 4.1.4).

I'm dealing with a pipeline that includes tools do not support Java 8 anymore, and being able to run it on Java 11 would be really useful, and GATK is the only package 'holding' this back. I did a search on the GATK github repo issues for bug reports for Java 11 and didn't really see anything recent which suggest to me this should (hopefully) be pretty stable.

The only issue here is that that the Spark compatibility might be affected (See GATK #6671 and #6053), but again I don't see any major incompatibility reports with Java 11.

I don't know what bioconda's approach to 'beta' stuff like this, so I make this as a proposal, and updating the build as it is not a new version of the tool.

Note that I've changed the requirement pinning structure to remove the more than operator, based on following the conda documentation here and here.

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[jfy133]

Neither , not | worked for some reason to separate different possible versions.

Despite 9 and 10 versions of java were never released for production use, unfortunately the recipe picks up the conda-forge version of openjdk which includes these version (which are not supported by GATK AFAIK), so using less than/more than doesn't work here.

[jfy133]

@BiocondaBot please add label

[apeltzer]

@bioconda/core any thoughts on this one?

[bgruening]

I am hesitant to include something that is not supported upstream. @jfy133 why are you not using separate environments? You can not support a one-fits-all environment for eternity. So I guess it's better to decompose your pipeline into separate envs.

[jfy133]

I am hesitant to include something that is not supported upstream. @jfy133 why are you not using separate environments? You can not support a one-fits-all environment for eternity. So I guess it's better to decompose your pipeline into separate envs.

@bgruening thanks for your input, and is what I expected.

You have a good point about that and I just conferred with @apeltzer and actually it is a misunderstanding on my part - apparently nextflow/nf-core pipelines do support separate containers per process (I thought that was only in a cutting edge version). So I will investigate that instead. Thanks anyway!