Correct issue in upgrade path for bwa

Need to improve this in future releases
Correct hash ref keys request

Fixes #33, identified at compile time by perl 5.18, previously only on access. Not used by submission code.
Sorted and added BTCA-SG
moved testData into t/data to clean up the structure
Clean up the logging and indicate executed command in log files
retain logs after execution
missing from ignore
Release for 1.0.3
Merge pull request #34 from ICGC-TCGA-PanCancer/dev

v1.0.3 - maintenance release