Align parabricks subworkflow

[famosab]

PR checklist

Closes #6894

• 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.
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• 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

[maxulysse]

where do you pass this downstream?

[famosab]

I planned to emit it in the end, its not needed for applybqsr though.

[famosab]

@sateeshperi Do you have any idea why the fq2bam process seems to not produce the expected output bam files?

[edmundmiller]

Should we maybe do a

Suggested change

	// Parabricks’s fq2bam requires 24GB of memory.
	// Parabricks’s fq2bam requires 24GB of memory.
	// resourceLimits = [cpus: 6GB, memory: 24.GB]
	memory = '24.GB'

https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam.html#man-fq2bam

Also it would be awesome to do some thing like --memory-limit ${task.memory} / 2 by default or make sure there's 16 cpus per GPU requested.

Just trying to push the resourceLimits syntax to the limits here 😆