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
HaplotypeCaller: ensure depth annotated in output VCFs and turn on GATK 3.1 hardware optimizations
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Improve automated tests to include mapping reads in chr22. Enables multi-chromosome and chromosome exclusion tests #370
Ensure extra haplotype chromosomes excluded from analysis regions if found in non-callable blocks. Avoids calling in these regions if not in variant_regions. Fixes #370
Update main.py

By default on Mac OS X the maximum number of files a process can open is 10,240. Unless the number 50,000 was chosen for a good reason, I suggest we change `target_procs` to `10240` to ensure a better out-of-the-box experience for Mac users.

The alternative would be to add a check for OS X before lowering `target_procs`.