Parabricks bulk update: Upgrading modules to Parabricks version 4.6

[gburnett-nvidia]

PR checklist

Closes #XXX

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[famosab]

except for this where we might need @mashehu for approval I think it looks good!

[mashehu]

That's quite a lot larger. Any way to make the test data smaller or what is causing this bloat?

[gburnett-nvidia]

The current solution is to change it back to g4dn.xlarge before pushing to main (see the note in the README.md). Only starfusion and rnafq2bam have this higher requirement and it comes down to system memory. Even with the smallest test data possible, the memory on the g4dn.xlarge is not large enough.

The minimum system requirements for Parabricks are 100 GB of memory for 1 GPU so this instance matches that, although for most of the tests it looks like we can get away with less.

Is this satisfactory for now?

[mashehu]

The current solution is to change it back to g4dn.xlarge before pushing to main

you mean you will switch this value back in this PR before merging or what do you mean with "pushing to main"?

[gburnett-nvidia]

Yes for now I will change it back before merging so I can unblock this PR until we can think of a more permanent solution. I will do some testing on smaller instances to see if I can size it down to a 4xlarge or 2xlarge, but I know the 1xlarge won't work.

[mashehu]

Sounds good

[gburnett-nvidia]

I finished my testing and everything was able to run on a g4dn.2xlarge, meaning that Parabricks is using 15-30 GB of system memory for the rnafq2bam module. I'd like to continue the discussion (maybe as a GitHub issue?) about if there's a better solution to testing this than having to manually change this in the nf-test-gpu.yml.

@famosab is there anything else you need to approve this PR or the starfusion one since they are both blocked by this issue?