Merge pull request #384 from mjafin/master

Modified SID settings to allow up to 10k coverage and lowered AF thresho...
Fixes for nglims-based sample preparation: correctly specify upload directory for Galaxy, handle controls, and avoid passing empty fastq files through
Improvements for Galaxy upload: handle creation of missing Galaxy database libraries, support nglims-based specifications, avoid uploading indexes
Entry point for creating validation plots from existing CSV files
fixed typo
Merge pull request #388 from kern3020/master

fixed typo
Ensure de-duplication occurs on Standard processing pipeline if specified
Add min_allele_fraction that customizes minimum detection ratio for tumor/normal calling. Used in MuTect indel detection but not generally yet. Provide hook to get tumor algorithm configuration #314
Do not merge nglims samples based on descriptions, only on unique names. Set parameters for standard nglims post-analysis to include de-duplication.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Update mutect.py

I had a copy-paste typo on line 114, apologies
Merge pull request #390 from mjafin/patch-2

Update mutect.py
Improve plotting of validation calls to handle whole genome inputs. Generalize plot normalization to keep consistent differences across plots.
Add proper NM and MD tags to STAR alignments.

Thanks to @mjafin for the suggestion.
Restore AS tag to STAR alignments.