Document new genome resource files and update details about handling these in the code
Retrieve sample description from input BAM file if not specific in configuration YAML. Move normalization and absolute path generation of input files into configuration file parser. Thanks to @tanglingfung
Improve version retrieval process for GATK: use initial cached versions instead of running command line version check. Requires a single re-run of versions on restarts but avoids intermittent errors with java -jar style version retrieval
Update exome multi-caller analysis with latest NA12878 reference materials. Provide better configuration file that runs out of the box with instructions, including allowing relative paths in input YAML.
Bump ipython-cluster-helper version to get fixes for Torque and PBS memory usage
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Enforce indexing following alignment to avoid multiple index runs at subsequent parallelized steps
Provide larger memory values for retrieving versions in GATK/Picard since that is now a one time operation. Try to avoid issues on MacOSX #98
Reorder validation step to work with multiple variant callers
Avoid scaling down jobs by total items until memory requirements applied. Prevents underscheduling of jobs with higher memory requirements
Include automated validation of ensemble calls as part of standard NA12878 validation workflow.
Clean ups on exome example documentation
Bug fixes for typo in VariantRecalibration and incorrect normalization in algorithm variantcaller parameter. Speed up for re-starts by avoiding initial version detection for GATK/Picard
Merge remote-tracking branch 'upstream/master' into varscan-paired
Add sample definitions for a VarScan run
Merge pull request #68 from lbeltrame/varscan-paired

Initial support for paired variant calling using VarScan
Increase default value for numBadVariants for VQSR of indels. Needed in 2.7 versions even for whole genome analyses
Clean up testing of cancer tumor/normal pairs for new varscan support #68. Improve handling of edge cases with empty call files.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Force US_en LANG for VarScan runs to avoid any locale specific errors in VCF output. #97