Add halo_pipeline shell script
Update pipeline, add mate-syncing script from Agilent
Update base recalibration to use correct parameters
Update halo_pipeline.sh to version that works with test files
Move files to experimental. Update options in halo_pipeline.sh
Add VariantEval step
Add pm functionality to setup halo shell script
Implement staging directories for analyses
Add vcf_summary
Merge remote branch 'origin/develop' into feature/halo-pipeline
Add config and setup options, make run_halo return dictionary
Merge branch 'feature/halo-pipeline' into develop