How to specify input resfile for Rosetta?
The problem is my pack.xml specified a resfile.txt location which over-wrote my command-line option.

    &lt;TASKOPERATIONS&gt;
       &lt;ReadResfile name="Design_Resfile" filename="resfile.txt"/&gt;
    &lt;/TASKOPERATIONS&gt;


If you remove the filename option in the XML file, you are then able to specify the path.

    &lt;TASKOPERATIONS&gt;
       &lt;ReadResfile name="Design_Resfile"/&gt;
    &lt;/TASKOPERATIONS&gt;