Support for TopHat 2.0.9: handle extra paired end output with single-mate matching secondary results. Filter these prior to continuing the pipeline. Thanks to @mariogiov for report
Merge pull request #11 from chapmanb/master

Support for TopHat 2.0.9: handle extra paired end output with single-mat...
Merge branch 'master' into kalkyl_test_config
Move checks for GATK VariantRecalibrator specific files to immediately before use. Enables standard hard-filtering of non-human organisms during variant calling
Default to solexa-quals if no quality format is provided.
Added note about default quality encoding for Tophat.
Update mm10-resources.yaml
Improve persistence of parameters passed on bcbio_nextgen install and upgrades to facilitate more cusomtized installations
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Provide installation and upgrade options that enable commerical and data-intensive tools. Fixes #111
Avoid using python environmental variables when running bcbio_nextgen.py, avoiding issues where PYTHONHOME or PYTHONPATH point to other library locations
Ensure ensemble variant calls get snpEff annotations for feeding into gemini database
Avoid OS errors due to too long argument lists for samtools merging: create shortened symlinked files to real files and pass those on commandline. Thanks to @brentp for report
Streamline VM creation process on VirtualBox
Sort the pairs output files before giving them back.

Some of the downstream tools expect paired FASTQ files to be
in order.
Make tophat look in rnaseq/tophat for the index files.

Also look for an index ending with _transcriptome.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Avoid update errors for existing installations with pre-existing install config YAMLs
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Release v0.7.3