Add parabricks/fq2bam as alternative to fastq_preprocess_gatk

[famosab]

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This adds the fq2bam tool from parabricks to the pipeline. Also renaming the gatk subworkflow to reflect that it does complete preprocessing and not only alignment.

Related to #1853.

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[maxulysse]

You'd need #1835 to be merged for tests

[famosab]

@maxulysse Did you discuss with @FriederikeHanssen about the nvidia containers and if we can use them like this?

[FriederikeHanssen]

Shall we merge this and update the container separately?

[FriederikeHanssen]

@famosab just check out your branch to work on some sentieon related refactoring with the new structure. I noticed this line: https://github.com/nf-core/sarek/blame/c9332a0a96414082d28b1d784c158a3f3dc3efbe/workflows/sarek/main.nf#L230 from you. Is there anything that should be cleaned up here before we merge in parabricks or possibly revert the first refactoring PR that enabled the parabricks implementation?

[famosab]

@FriederikeHanssen Just remove that comment, that was me being stupid and I forgot to remove the comment 😁 I don't think there is anything else.

[maxulysse]

Sorry, once again, I'm going to ask you if you could sync with dev.
That should get rid of the currently failing pytest