Merging development branch from Malaria project - decontamination, pipelines for organisms with no variant truth set, etc.

[brosula]

Merging work based on the development I have been working on for the short read malaria project. Most updates are in line with jts_updates_for_malaria_joint_calling branch as of 4/23/2024.

Major updates:

1. Addition of "bootstrap" WDLs to support the processing of organisms without a variant truth set.

• SRWholeGenomeBootstrap.wdl - Disabled VETS
• SRJointCallGVCFsWithGenomicsDBBootstrap.wdl - Disabled VETS

2. Addition of bowtie2-based decontamination

• SRFlowcellDecontaminate.wdl - Add "aligner" as a parameter that can take "bwa-mem2" or "bowtie2"
• SRUtils.wdl - Added bowtie2 task for alignment

Minor updates:

1. FunctionalAnnotation.wdl - Added support for non-Plasmodium reference genomes
2. VariantUtils.wdl - Added various tasks, such as hard filtering by GATK defaults
3. HaplotypeCallerBootstrap.wdl - Added to support SRWholeGenomeBootstrap.wdl (although it is largely similar to HaplotypeCaller.wdl)
4. SRReblockGVCFs.wdl - Added standalone reblocking workflow to process (g)vcfs produced by HaplotypeCaller when ReblockGVCFs was disabled.