Trgt 1.2.0

[Schmytzi]

Closes #298. Removed local TRGT module and replaced it with trgt/genotype from nf-core.
Also replaced call to bcftools/merge with trgt/merge because bcftools drops most of the REF allele.

PR checklist

• This comment contains a description of changes (with reason).
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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).

[fellen31]

Nice! When I had a look previously, updating TRGT beyond 0.7.0 or something broke stranger. But perhaps this is not the case anymore?

[fellen31]

Also, if we add a tool for ONT-data, any ideas on how those calls should be merged if not with bcftools? I believe nf-core/raredisease uses SVDB merge.

[Schmytzi]

Nice! When I had a look previously, updating TRGT beyond 0.7.0 or something broke stranger. But perhaps this is not the case anymore?

As far as I can tell, it worked fine. I didn't check whether the annotations are the same, though.

[Schmytzi]

Also, if we add a tool for ONT-data, any ideas on how those calls should be merged if not with bcftools? I believe nf-core/raredisease uses SVDB merge.

I guess, if we process ONT data, we'd exclusively run the other tool, wouldn't we? Maybe there's a tool that works better with whatever becomes our ONT tool

[fellen31]

I guess, if we process ONT data, we'd exclusively run the other tool, wouldn't we? Maybe there's a tool that works better with whatever becomes our ONT tool

What I meant was that it would be nice if we could still merge using the same tool, regardless of the caller. But we can take that when we get there.

[fellen31]

Nice, I tested your branch and it seems to work well.