Adding in some mutation testing code
Adding in some workflow changes
Massive reorganization
Refactoring to share docker images
Working on the new docker based command calling
Porting the original shell script pipeline to python
Working on the different docker build and debugging the chain runner
Fixing bugs as I work on the icgc alignment pipeline
Adding in the docker build
Merge branch 'dev' of github.com:kellrott/tcga_realign into dev
Adding test file for icgc-align pipeline
Working on the ICGC BWA aligner code
first (unfinshed) pass at simpleflowing the upload
working now, still needs more testing
Adding multiprocessing
Adding PI field to read group header only if it is defined
fixed new line in the elif not live error str
Working on the merging code
Merge branch 'dev' of github.com:kellrott/tcga_realign into dev
Working on merge code