Add subworkflow: gatk joint germline calling

[GCJMackenzie]

PR checklist

Closes #1126

Adds joint germline variant calling subworkflow. Based on Gatk best practices for joint germline calling. Do not merge until the checklist in 1126 is finished

• [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
  • [x] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd
  • [x] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd

[GCJMackenzie]

Won't be able to merge it in until the cl tests are back up again. But here is where it is so far

[lescai]

wonderful wonderful! thanks everyone for the hard work on this!!

[FriederikeHanssen]

Oh on problem I see now, is that I updated a bunch of gatk modules over Christmas , that use intervals, because we usually have multiple intervals per patient. Sorry about that. So I believe the input for some of them need to be adapted, like Haplotypecaller for example will have the interval within the input (sorry about that @GCJMackenzie 😢 )

[matthdsm]

Hi there!

We've noticed there hasn't been much activity here. Are you still planning on working on this? If not, you can ignore this message and we'll close your PR in about 2 weeks

Cheers the nf-core maintainers