Merge remote-tracking branch 'central/master'
Merge conflicts
Add halo_pipeline shell script
Update pipeline, add mate-syncing script from Agilent
Merge conflicts, mostly from my whitespace removals
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
Merge pull request #201 from brainstorm/master

Weekly develop-->master merge
Add VariantEval step
improved robustness of miseq samplesheet parsing
Merge branch 'develop' of github.com:SciLifeLab/scilifelab into develop
corrected samplesheet entry for missing index sequence
Add pm functionality to setup halo shell script
-