More bug fixing and --retry_failed option for piper runs

@mariogiov give a look to recreate_project_from_filesystem for now I have fixed it but I think you want to go through the various parameters and change their names or do some validation before run the command 
I hadn't seen this before - but a quick comment is that you only need the switch for the last step to run. So for do variant calling you only need `--variant_calling`, and everything before that will be run as needed.