Annotate and rank SNVs per family

[fellen31]

This PR:

• Annotates and ranks SNVs per family instead of per project. This is because genmod does not support compound scoring with multiple families in the VCF. Someone that still wants annotated variants per sample can run each sample as a separate family.
• Changes the output documentation and structure to match sample and family for all variants
• Puts the validating of the samplesheet into functions, and removed the use of ifEmpty. This is because these error messages would always show up when you had an error, even if that error was unrelated.
• Removed support for automatically creating an echvar database with SNVs and INDELs, since this requires all variants to be combined into one VCF. Might add this back into the future.
• Removes the containts_affected logic from the snv-calling workflow, since this was previously changed to be checked before pipeline start, and is now done in one of the functions described in point 3.

Closes #501 and #276.

PR checklist

• 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 pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
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• 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).

[Lucpen]

Just a tiny typo and one question:
why not make a switch for this?
Removed support for automatically creating an echvar database with SNVs and INDELs, since this requires all variants to be combined into one VCF. Might add this back into the future.

[fellen31]

Just a tiny typo and one question: why not make a switch for this? Removed support for automatically creating an echvar database with SNVs and INDELs, since this requires all variants to be combined into one VCF. Might add this back into the future.

My idea initially was that it would be nice if you could create a reference database or panel of normals while running the pipeline. For SNVs and INDELs, yes it would be fairly easy to make a switch. But we need to add a module to merge VCFs together before creating a database (and then it should really be a workflow).

But for creating SVs, CNVs, STRs and methylation databases we would need a different merging strategies. It would perhaps be nice, but I need to think about it some more. It might work for a 100 samples, but perhaps you would never want to start 1000+ samples at once, and then creating the databases within the pipeline becomes unnecessary, because you would need to combine samples from multiple pipeline runs anyway.

In short, I'm removing the functionality because it's easier at the moment. It's not something that we need in production, and not something I'm sure is desirable to have in the pipeline in the future.