Add new version of joint germline subworkflow. Early WIP

[GCJMackenzie]

PR checklist

• This comment contains a description of changes (with reason). Adds the new version of the joint germline subworkflow, used for adding gvcf files to a genomicsdb workspace, then perform joint variant calling using genotypeGVCFs. New version separates this step from haplotypecaller and the vqsr process. Whilst the code is functional with in Atholl, there is some work to do to bring it in line with Sarek guidelines. It is not ready for review currently. Adding PR now for tracking purposes. Linked to issue Enable joint variant calling for germline samples #75.
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[maxulysse]

I marked this as a draft as it's a WIP

[maxulysse]

Closing this one in favor of #595