Add germlinecnvcaller

[ramprasadn]

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
• If necessary, also make a PR on the nf-core/createpanelrefs 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 --outdir <OUTDIR>).
• 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]

We should emit the output from GATK4_GERMLINECNVCALLER as well

[ramprasadn]

We don't really be using the output anywhere else that's why I didn't add it here.. Don't mind doing it, but I am curious to know your reason. Is it just good practice? Or there are other reason we should do it?

[maxulysse]

I'd say good practice (plus some other ideas I'm trying to work in)
I need to check I'm actually doing that in the other subworkflows...

[ramprasadn]

Cool! I will add it 👍🏻

[maxulysse]

Looking good, I'm almost considering pushing your subworkflows to nf-core/modules

[ramprasadn]

I don't think this cohort mode analysis will find use in other pipelines, since its something an user will run occasionally to create references.. In that case, its probably easier to use this pipeline to create those files.. But this workflow calling cnvs in case mode could be of use to others.. I can polish that one a bit and add it to modules.