Add halo_pipeline shell script
Update pipeline, add mate-syncing script from Agilent
Add date to best practice document
Add custom delivery path and add vcf.gz and tbi files to delivery
Update base recalibration to use correct parameters
Add option to deliver subset of bam files. Include tsv files in best practice delivery
Update halo_pipeline.sh to version that works with test files
Fix merge conflict
Update hs-metrics and vcf-summary functions. Make workingDirectory default os.curdir
Move files to experimental. Update options in halo_pipeline.sh
Add VariantEval step
Add pm functionality to setup halo shell script
Merge pull request #202 from mayabrandi/develop

minor chanages
Merge pull request #204 from mayabrandi/develop

Adjusted for config file in funk_001. This verssion works from funk_001
Implement staging directories for analyses
Add vcf_summary
Merge remote branch 'origin/develop' into feature/halo-pipeline
Merge remote branch 'origin/develop' into develop
Add config and setup options, make run_halo return dictionary
Merge branch 'feature/halo-pipeline' into develop