Java (picard) -Xmx parameter

[tdayris]

Hi,

I was wondering if this is a good idea or not: based on the resources parameter in snakemake rules, then build -Xmx parameter automatically for any java tool that allow this kind of parameters.

Here, the conda wrapper of almost any picard subcommands handles -Xm*, and -D* options, so Xmx is handled.

If you agree with this, I am willing to do the same in Picard, SnpSift, SnpEff, GATK and Trinity (max_memory). If you see any other tool that would need such changes, please tell me and I'll be happy to make the changes.

Thanks in advance for your reviews.

PS: The modifications in generate_docs.py come from a PR i did this morning. I don't know how to hide it since it has been already accepted.

[johanneskoester]

This is an awesome idea, I would very much welcome it!