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rosrun itself doesn't load parameters. rosparam is the tool for that. Basically the command is the same like in the lauch file, you'd only need to take care of pushing things into the node's namespace, e.g.

<rosparam command="load" file="$(find cfg_pkg)/cfg/common_costmap.yaml" ns="global_costmap">

->

rosparam load $(rospack find cfg_pkg)/cfg/common_costmap.yaml my_node_name/global_costmap

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