GATK UnifiedGenotyper Fix due to Broad Website change

[jfy133]

Unfortunately, GATK have removed the ability to (easily) download the old jar with their new website. GATK 3.5 might actually be 'lost' now.

I have changed the system to require the user to supply their own JAR, if they want to use UnifiedGenotyper. Accordingly, I've removed the UG (and downstream tools requiring UG) github actions/travis test for now. Can consider replacing some downstream steps (e.g. vcf2genome with bcftools consensus - https://samtools.github.io/bcftools/howtos/consensus-sequence.html).

I may have a lead where could alternatively download the JAR (and add to the github actions step a download command), but waiting for feedback from Broad.

Important The failure to download UG is why the other PRs are currently failing, this will need to be merged first.

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!
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated

Learn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md

[jfy133]

Alternatively could switch to the new (now they've fixed it), storage location: https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk

But I don't trust them anymore ;)

[jfy133]

New download location avaliable for GATK 3.5 from here

I've kept new JAR system for EAGER, but re-enabled tests (hopefully) with a pre-run download step in github actions workflow.

[apeltzer]

I actually love that they moved things to a better (stable) URL :-D

[jfy133]

Unfortunately still couldn't get the tests to work, but will hopefully do it soon.

I agree!