made metadata changes based on OICRs example metadata discussed at the 7/24/2014 telecon with Brian
added a test analysis template file to be used with PCAWG_TEST study
Merge branch 'master' of ssh://github.com/kellrott/tcga_realign into dev_cwilks1

catching up with Kyles master changes
fixed how parameter test is pulled, now has the default of False
added set -e; set -o pipefail; to piped commands in bam_utils and bwa_mem, added an exit_code check on the rg headers processing command in bam_utils
Merge pull request #11 from kellrott/dev_cwilks1

made metadata changes based on OICRs example metadata discussed at the 7...