REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:
I have pull gatk using docker, however, every time I use gatk, I have to go into the container to run the software. The guidance told that I can set the shell path when open the container, but it cause big problem when I have mutiple files located in different paths of shell. Is there some ways that can run the gatk outside the containcer? Or other ways that can slove this problem?
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