Partially created files are used for resume a run #78
Description
Describe the bug
In some cases there are particular steps such as the SORTBAM that even if not fully complete they are writing the final file that will then be outputted by the process in such a way that when the run is resumed this temporarily unfinished file is used for the downstream steps, leading to problems of integrity of the files
To Reproduce
- Start running any run
- Stop it or cancel it midway through, usually I expericence this when the run is cancelled by external reasons...
- Resume the run and you will see that some of those partial files have been passed onto the next step
Expected behavior
The unfinished file should be removed or something should happen to it to make sure that it is not taken by the downstream processes unless it is complete.