Feature Request: Add resume logic option to pick up from individual pipeline steps

[Alfredo-Enrique]

Key feature request: To make the pipeline more robust and functional, we need to add additional logic that allows us to resume processing if individual pipelines that have not finished. As of right now, users might be tempted to relaunch the pipeline from the start if some of the individual downstream pipelines errored out (eg. call-mtSNV, call-sSV). As of now, users need to manually check outputs, and if something fails in a downstream pipeline, they have to make new individual inputs and group configs for all these samples.

A more harmonious/functional approach is to add logic to :

1. Check if the individual pipeline steps are finished and copied the sample to /hot
2. If No, relaunch this individual patient/sample group from the last pipeline not completed.

This will especially be useful in case of cluster instability, as we can just resume from later steps, and free up user time.

[Alfredo-Enrique]

@zhuchcn @yashpatel6 Let me know if I missed anything from our discussion!