DNA-seq disambiguation enabled
Merge pull request #260 from mjafin/master

DNA-seq disambiguation enabled
Include all samples in project-summary when multiple pipelines specified in the same file. Thanks to @mjafin #260
Sample a maximum of 1000000 reads for the complexity calculation.
Avoid extra coordinate sorting step when fixing input BAM fix run groups. Thanks to Severine Catreux
Add rnaseqc to the resource requirements.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Update process_alignment resources to match ipython specifications
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Have final BAM index file in upload directory use the more common .bam.bai extension. Fixes #261