Initialize reports job success even when sample is incorrectly initialized
As has been seen in a recent Skype discussion in the HWWAnalysisCode development, when submitting initialize jobs, the job seems to report as succeeded even when a sample fails. There's two requests for change here:
- Because this seems to be related to an unfortunately common case, whee a hidden file artifact is left behind from the rsync process, it would be nice if initialize would not try and initialize hidden files (ones that begin with .), and then maybe and INFO or WARNING message can be sent to the user notifying this file was skipped.
- When a sample folder does not initialize completely, no file should be written. This will cause the batch systems to report this job as a failure rather than a success. An added layer of protection here could include a failure in tqmerge when merging an incomplete sample folder, but this is less necessary than the batch reporting the failure.