fix for issue #494
chanjo integration
issue #249 - chanjo integration
Merge branch 'dev' - chanjo integration
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
polish fix for issue #494. add unit test
moved chanjo test stub to test directory
renamed variable based on code review
specify version for chanjo
Merge branch 'master' of https://github.com/kern3020/bcbio-nextgen
extended notes on how to run a stub pipeline for chanjo
Merge requirements
Merge branch 'kern3020-master'
Move to using new shared conda collections for installations. Cleanup of coverage integration
Merge pull request #505 from mjafin/master

Fixed downsampling for mutect to use Broad default when max_coverage_dep...
Clean up RNA-seq tests. Generalize QC detection slightly to run correct quality control for RNA-seq and ChIP-seq on derived pipelines starting with correct prefix
Fix for Tophat setting the insert size as the inner distance size.