Add GATK/Picard tasks for generating WGS qc metrics

[mark-welsh]

For UI issues

• Tool: Picard
• Version: 2.19.0

Description

WGS pipelines are long and therefore can have a high degree of variability across runs. Picard has many commands for generating QC metrics and md5s that will help maintain integrity/traceability.

What I Did

add task wrappers for:

• [x] CalculateReadGroupChecksum
• [x] CollectMultipleMetrics
• [x] CollectQualityYieldMetrics
• [x] CollectVariantCallingMetrics
• [x] CollectWgsMetrics
• [x] ValidateSamFile

[mark-welsh]

also going to add GATK ValidateVariants as a part of this