Fixed downsampling in MuTect to match that of coverage_depth_max
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
Merge remote-tracking branch 'upstream/master'
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
Merge remote-tracking branch 'upstream/master'