Add vqsr subworkflow Work In Progress

[GCJMackenzie]

PR checklist

• This comment contains a description of changes (with reason). Adds the variant quality score recalibrator subworkflow, used for recalibrating joint germline variant calls. 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 Do VQSR for HaplotypeCaller calls #89
• 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).

[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

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Hi @GCJMackenzie,

It looks like this pull-request is has been made against the GCJMackenzie/sarek master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the GCJMackenzie/sarek dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[maxulysse]

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