Avoid errors when Galaxy location files contain the same genome multiple times. Use the most recently added genome. Fixes #360
Drop header to a lower level.
Avoid downscaling on IndelRealigner which needs full memory for handling deep sequencing regions. Thanks to @mjafin
Merge pull request #362 from mjafin/master

Fixed downsampling in MuTect to match that of coverage_depth_max
Ensure tumor samples passed along during variant grouping to avoid stray normal-only samples on re-runs. Fixes #356. Correctly prepare single sample gemini VCF files
Filter BED regions when subsetting by minimum size instead of trying to adjust size. This handles issues at the ends of chromosomes which cause out of range errors in FreeBayes
Add AlienTrimmer to the resource requirements for trimming.
v0.7.8
Move solexa namespace to illumina (finally) and start to clean up API
Create a sequencer sub-command to replace older sequencer integration scripts. Initial framework for detecting dumped Illumina runs and creating a samplesheet from nglims inputs
Use Illumina's bcl2fastq to demultiplex and prepare fastq files from raw Illumina machine bcls
Ensure system configuration and manifests created prior to adding toolplus targets on new installation. Fixes #366
Update cosmic to v68. Fixes #365. Use bgzipped dbSNP and other Broad bundle inputs
Update bcbio_nextgen.py

I think the example configuration file has changed.
Update installation.rst

Fix typo in docs.
Merge pull request #367 from hammer/patch-1

Update bcbio_nextgen.py
Added @hammer
Merge pull request #368 from hammer/patch-2

Update installation.rst, thanks to @hammer
Update README.rst

My Mount Sinai affiliation probably makes more sense for contributions to this project!
Merge pull request #369 from hammer/patch-1

Update README.rst