Added GATK genotyping modules.

[jfy133]

This includes modules for genotyping (VCF creation) with GATK UnifiedGenotyper and GATK Haplotyper caller.

Note: GATK UnifiedGenotyper firstly downloads the GATK 3.5 jar file, which has the last working version of GATK used in EAGER1 @MPI-SHH. Pathogen people at MPI-SHH currently require the specific VCF format from 3.5 as later versions modify this and does not work with a downstream tool currently.

The implementation mostly matches EAGER1 functionality other than the 'additional parameter' flag. Not included is ANGSD or SNP filtering.

(Sorry for messy/too many commits; this was a learning experience for me ;))

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 necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo [NOT REQUIRED]
• Ensure the test suite passes (nextflow run . -profile test,docker) [RAN WITH OWN TESTS].
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated [NOT REQUIRED]

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

[apeltzer]

We need to have a separate entry in the scrape_software_versions.py script to parse the GATK3.X version information, too.

[jfy133]

Added, and the pipeline runs through 'successfully' but I don't see any output from that script? There isn't an error in the .nextflow.log to suggest it failed either...

[apeltzer]

Thanks for your edits, I'll merge this to branch GATK-UG so we can jointly update this to get it out very soon 👍