Add picard metrics to halo pipeline
Update haloplex workflow image
Add information about HaloPlex command
Update image and config file
Add lib
Update module paths from ratatosk.* to ratatosk.lib.*.*
Update ratatosk lib paths, fix bug in bwa aln for paired target dependency
Merge branch 'feature/move_applications_to_lib' into develop
Update documentation to reflect module reorganization
Minor edit to README
Remove cement dependencies
Update docs
Reimplement IndelRealigner to have as main parent task an input bam file
Cleanup code; remove redundant opts, requires, and output functions
Correct trailing options errors (non-lists), hsmetrics arguments, missing references in gatk programs
Merge branch 'feature/use_executable_name' into develop
Update tests, add target_generator functions to allow for site-specific config
Remove scilife-specific code
Update run_ratatosk examples
Minor modifications