Calculate variant caller reference disk storage in WDL

Calculate variant caller reference disk storage in WDL
Remove unneeded disk storage calculation from checker WDL

Convert parameterized JSON local paths to GCS paths

Convert parameterized JSON local paths to GCS paths

TopMed workflows with variant caller checker and concordance workflow

Added checker workflow for U of Michigan variant caller
Added U of Chicago VCF concordance workflow

1.8.0

Added U of Michigan official aligner
Added U of Michigan official aligner checker
Added Functional Equivalence CWL
Added Functional Equivalence CWL checker
NA12878 test files
Script to generate input JSON

1.6.0 Add subdir for aligner and put release in checker path

Added a subdirectory for aligner workflows
Put the release tag in the raw path for the checker workflow WDL

1.5.0 Remove options file

Remove WDL options file since it is not supported by FireCloud
Use variable for docker image

1.4.0

fix disk size for alignment checker

1.3.0 - Modified freeze3 variant caller to use b38 reference

Moved variant caller files to their own subdirectory
Added Dockerfile for variant caller that pulls a specific commit from the U of Michigan freeze3 git repo
Changed the variant caller WDL so it alters reference file paths in the config files to accept a b38 reference genome

1.2.0

Add alignment caller checker workflow
Move variant caller workflow to its own subdirectory
Add a Dockerfile for the variant caller that uses a commit in the U of Michigan git repository
Add WDL for the variant caller that modifies the configuration files to accept b38 reference files

1.1.0

Added variant calling WDL and input JSON