Add gatk cnvcaller

[ryanjameskennedy]

PR checklist

Adds gatk's germline cnv caller modules (PreprocessIntervals, CollectReadCounts, AnnotateIntervals, FilterIntervals) and the respective test files

• [x] This comment contains a description of changes (with reason).
• [x] If you've fixed a bug or added code that should be tested, add tests!
• [x] If you've added a new tool - have you followed the module conventions in the contribution docs
• [x] If necessary, include test data in your PR.
• [x] Remove all TODO statements.
• [x] Emit the versions.yml file.
• [x] Follow the naming conventions.
• [x] Follow the parameters requirements.
• [x] Follow the input/output options guidelines.
• [x] Add a resource label
• [x] 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:
  • [x] PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • [x] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • [x] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

[ryanjameskennedy]

Some of gatk's germline cnv caller modules (PreprocessIntervals, CollectReadCounts, AnnotateIntervals, FilterIntervals) and the respective test files were added. Other modules (DetermineGermlineContigPloidy, GermlineCNVCaller, PostProcessGermlineCNVCalls) are unable to be tested as the biocontainers used by nf-core for Singularity and Docker do not contain gcnvkernel.

[jfy133]

@ryanjameskennedy small tip for the future: it would be good to split these up into one PR per module as you will get speedier responses from more people, having to review so many modules in one go will put a lot of people off

[nvnieuwk]

@ryanjameskennedy what's the status on this PR?

[ryanjameskennedy]

It's not yet finished, I have changed it's status to a draft.