lumpy structural variation detection with bwa-mem input on paired and split reads. Implement detection of necessary metrics and running lumpy
Ensure flowcell and sample YAML paths entered on commandline are normalized to the absolute PATH. Avoid requirement to specify input on commandline for whole genome example
Merge pull request #158 from mariogiov/master

Add configurable species resources directory
Move species resources specification inside general  configuration. Document usage. #158
Recursive config file traversal to expand all shell variables
Merge pull request #14 from chapmanb/master

Merge from Brad upstream
Merge branch 'recursive_shell_expansion'
Merge branch 'master' into kalkyl_test_config