Parabricks haplotypecaller version update and tests migrated to nf-test

[Furentsu]

PR checklist

Parabricks haplotypecaller was updated to latest version (4.4.0-1) and tests were migrated to nf-test.

• 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]

@Furentsu I added a few comments. Are you able to run the tests locally to create the snap?

[mashehu]

@nf-core-bot fix linting

[Furentsu]

I tested on our HPC with a GPU but I get the "Could not find accessible GPUs" error.

[famosab]

I tested on our HPC with a GPU but I get the "Could not find accessible GPUs" error.

For me the current test profile also did not work. SO I changed again the docker.runPtions and just ran it with --profile docker (in tests/config/nf-test.config)

docker.runOptions = '-u $(id -u):$(id -g) --gpus device=0 --platform=linux/amd64'

[mashehu]

hmm, out of memory error. is that fixable on your side or do we need bigger instances?

[Furentsu]

@mashehu I have already added a flag for low memory usage, it should do.. on our HPC I get a different error that should be due to the test files used:

Chr chr21 not found in the reference. Exiting., exiting.

[Furentsu]

All tests are now passing on our HPC. I do not understand why they're not passing here

[famosab]

Linting fails because one of the tests produces an empty file (probably because no variants were called). So you'll either need to change the test data or the assertion :)