Merge branch 'release/v0.2.1'
Merge branch 'release/v0.3'
Merge branch 'release/v0.3.1'
update readme
fix merge conflict
revert to working pipe code
Merge branches 'master' and 'develop' into develop
fix gatk workflow parallelization
* Only use ReduceReads when -capture is off
* Replace fastqc with fastq-stats from eautils.  fastqc can't handle multiple input files, which is absurd
* Small bug fixes