Add additional documentation on 'coverage_interval' usage. Fixes #549
Merge pull request #550 from lpantano/upstream

related to kraken and qsiganture memory
Improve SNAP memory usage and avoid secondary alignments to improve performance.
Bump ipython-cluster-helper with mincores and cleanup improvements for development
Fix for matplotlib not connecting to a display.

Toggle plt.ioff everywhere before plotting.
Support variant calling for organisms without dbSNP files. Thanks to Mark Rose.
Improvements to java memory usage for VarScan and MuTect to help scale tumor/normal variant calling
Added proper readgroup information in bowtie2 alignment.
Closes #552.
Added @matted to the contributor list.
Actually add Matt to the contributor list.
Edge case fixes for somatic variant calling: FreeBayes somatic correction restarts when partially finished and scalpel region preparation from tuples
Add dependencies for cnvkit installation and provide target to only update conda deps
Initial work on CNVkit integration -- support for testing single sample calls (cc @etal)
Update speedseq lumpy calling to match command line arguments in latest version
Do not require cutadapt on PATH and use the command relative to Python installation. Fixes #561
Ensemble enabled for tumor-normal studies.
Enable streaming S3 input to RNA-seq and variant processing.
Fixes for GATK joint haplotype calling: correctly batch groups when using post-alignment preparation, provide useful error message when missing batches, filter stray NON_REF gVCF calls in GATK HaplotypeCaller output. Thanks to @lpantano
Update working with RNA-seq pipeline instructions
Fix data grabbing script to have a consistent name