Use vg WDL that gives RTG a defined memory limit

[adamnovak]

Changelog Entry

To be copied to the draft changelog by merger:

• vg CI should no longer fail with complaints from rtg

Description

This will hopefully fix the CI problem noted in #4916 (comment) where rtg will fail on the new CI runners for mysterious and possibly memory-limit-related reasons.

[adamnovak]

Setting up the memory limit in advance didn't help, but this should now avoid the failing step (building an RTG SDF template inside of hap.py) by just passing in the one the workflow already made.

Then I made a bunch of changes to fix problems I encountered trying to build the vg Docker and run the test outside of CI, which I never actually managed to do.

[adamnovak]

OK, the underlying problem is what was encountered at Illumina/hap.py#189 where rtg just always fails with null for nearly anything. (I guess except making an SDF?)

I can test for it with:

docker run -ti --rm quay.io/adamnovak/hap.py:v0.3.15 /opt/hap.py/libexec/rtg-tools-install/rtg index

(Or more or less any rtg command that isn't just help.)

When I run this on Courtyard it works. When I run this on our new Ubuntu 26.04 CI runners with kernel 7.0 and a similarly fresh Docker daemon, it fails.

It was suggested in Illumina/hap.py#189 (comment) that replacing the rtg in the container with version 3.13 might help. I think 3.13 needs a newer Java than we have in the container, but the example approach doesn't seem to bother updating it.