[FEATURE] Disabling JVM Hotspot in modules for JAVA tools

Is your feature request related to a problem? Please describe

I've encountered a problem with the JVM Hotspot for GATK processes when multiple GATK processes are run on the same node in singularity containers (details in nf-sarek issue #1030). There's also a recent Sarek issue with SIGBUS errors related to Hotspot (nf-sarek issue #1024).

Describe the solution you'd like

I'd like to proposed turning HotSpot off using -XX:-UsePerfData in the --java-options passed to GATK.

This has two effects - it should eliminate a class of bugs related to the JVM and hsperfdata, as well as stabilising nf-core Singularity modules in rare and hard-to-debug situations.

Describe alternatives you've considered

Hotspot is hard-coded in the JVM to write files to /tmp. It ignores the --tmp-dir flag passed to GATK.

As far as I can tell turning this off has no negative side effects beyond preventing the use of jstat and certain Java debuggers which don't seem to be used in nf-core. This detailed blog post from Evan Jones describes an improvement to Java GC efficiency from turning this system off.

Alternatives would include preventing singularity from mounting host /tmp into the container (I'm not certain how this might be achieved within nf-core), or using -XX:+PerfDisableSharedMem.

Additional context

I'm currently trialling nf-sarek with the -XX:-UsePerfData java option on ~100 human WGS and will update on stability.

The issue identifies GATK modules and the --java-options entry point, but no specific files or tests. Locate the Java-based GATK module definitions and inspect how those options are assembled. Done means the requested JVM option is applied to the intended modules and their relevant tests pass.