new subworkflow: gatk_joint_germline_variant_calling

[GCJMackenzie]

This subworkflow will cover the gatk4 best practices workflow: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- starting with the analysis ready reads of multiple individual samples*, haplotypecaller is then run in gvcf mode for each sample, the output gvcfs are then combined into a single genomicsdb workspace, and then run through genotypeGVCFs to perform joint germline genotyping and produce a joint vcf file. VQSR is then run to recalibrate the results file using variantrecalibrator and applyvqsr**.

* setting run_haplotc to false will skip haplotypecaller and use individual gvcf files as input instead, which go directly to genomicsdbimport. ** setting run_vqsr to false will skip VQSR recalibration, meaning the run ends with the output of genotypeGVCFs

• [x] This subworkflow does not exist yet with the nf-core modules list command
• [x] There is no open pull request for this subworkflow
• [x] There is no open issue for this subworkflow
• [x] If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module

[GCJMackenzie]

To Do list:

• [x] confirm updated test data is good to go and finish the PR
• [x] get variantrecalibrator reviewed and onto the nf-core modules repo
• [x] get applyvqsr reviewed and onto the nf-core modules repo
• [x] genotypegvcfs is missing an output channel for the tbi index, also needs updated to new test data and some other small tweaks, so make changes and get reviewed
• [ ] once all other to-dos are complete, review PR for joint genotype subworkflow and submit to modules repo