Adjusted CNVKIT/BATCH for germline mode

[SusiJo]

PR checklist

This PR enables the cnvkit/batch module to run in germline mode in addition to tumor_only and somatic mode.

• 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:
  • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
  • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

[FriederikeHanssen]

you don't need the funky ##idx## thing?

[SusiJo]

not if the fasta_fai is passed along with the fasta reference genome and both files are stored locally

[FriederikeHanssen]

ok I'll ask about this on slack

[SusiJo]

if both files are not local and are accessed instead via an https://, s3:// or other URL then the "##idx##" would be needed.