Stopping at HaplotypeCaller

[jcgrenier]

Thanks @dtaliun for putting this pipeline together!

I was able to get through the first steps of the pipeline correctly. I made some modifications in the command lines called since I'm using GLIMPSE v2 and some options are a bit different.
However, I'm only able to get log files from the chunk step in the result folder for now. I was able to do the HaplotypeCaller step as well, but then it stops without any error. I seems that the pipeline is not able to find the input files it needs in order to continue?

I also noticed that when I launch again the pipeline, it can't detect which steps ended up well. So it just starts again from scratch.
Can you help me with this?
Thanks a lot!
JC