Added support for STAR aligner based two species disambiguation
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Merge pull request #284 from mjafin/master

Support STAR alignment disambiguation for mixed species samples. Thanks to @mjafin
Gracefully handle failures when GATK creates an empty idx file during annotation
Rework initial fastq retrieval and gunzipping to work in parallel. Explicitly move this functionality to RNA-seq and ChiP-seq pipelines and remove duplicated checks. Remove outdated demultiplexing code. Fixes #281
Enable specification of samples in multiple batches: allows a single normal sample to match with multiple tumors. Attach variant calling output to tumor samples and avoid splitting tumor/normal into separate VCFs. Fixes for filtering: avoid ploidy post-filtering and GATK filtering on MuTecT output. #285
Do not require gemini to be on PATH for data updates. Thanks to Nishanth Dandapanthu
Support infrastrcture for passing single tumor-only and tumor with normal panel inputs to cancer variant calling. Provide test case for development. #285 #273
Added support for tumor-only calling and use of normal_panel vcf in mutect.py
Merge pull request #293 from mjafin/master

Added support for tumor-only calling and use of normal_panel vcf in mute...
Avoid reconstitution errors for single tumor-only inputs to variant calling. #293
Add globals option to sample input YAML files. Enables specification of shared files a single time making avoiding copy paste and making updates available. Automatically create globals in template functionality if present
Integrate validation plots into standard workflow. Currently requires manually installation of prettyplotlib into bcbio python site-packages until next release
Fixes global options being looked up by value instead of key.
Remove debugger usage.
Fixes: revert 457cd7641a with better documentation and checking for non-hashable values; sorry @roryk for the issue. Correctly ensure all samples are passed back from validation.
Ensure finding of cutadapt installed in local Anaconda python directory. Fixes #295
Ensure track and browser lines are removed from input BED file before feeding to SnpEff #216
Remove filterInterval passed to snpEff which can cause errors in some cases. Prefer filtering by regions done upstream. #216. Also includes small fix for latest GitHub prettyplotlib visuatlization
Bump to latest ipython-cluster-helper with LSF resource support and shorter tags. #258