Support command line runs within docker images: handle merging of docker local and global configuration. Allow specification of work directory
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
Added option of reporting gene_name instead of gene_id in htseq count files.