Single Sample Pipeline improvements

This pre-release of the single sample pipeline contains several improvements:

• PESR collection has been changed from svtk collect-pesr to GATK PairedEndAndSplitReadEvidenceCollection. This should fix a rare issue observed on some samples in which PESR records appear out of order and are not consolidated into single rows. (#34)
• Moves WDL parameters to the new nomenclature of include and exclude lists (#29)
• Fixes invalid VCF headers (#41)
• In the final single sample VCF output, reports reciprocal translocation events using a set of BND records linked by EVENT_ID (#36)
• Adds annotation with gnomAD allele frequencies to the Single Sample pipeline, and provides an additional output in BED format.

Hotfix 2 for v0.8

This fixes an issue in WHAM processing and standardization that stemmed from incomplete substituting of sample IDs that was causing all variants from WHAM to be lost.

Hotfix for v0.8

Fixes a small bug that prevented running the single sample pipeline on Cromwell instances with no local filesystem configured (including Terra's).

Pre-release for single sample pipeline

Fixes a bug in v0.8-beta that prevented the single sample pipeline from running when MELT reference-panel inputs were not given.

Aside from the single sample pipeline, the other pipelines in the repository are still not ready for release yet and should not be run in this version.