Post-processing steps need to access the results files of the external application. Thus, if you are running on a master-node setup, the directory you choose for these results files must be shared, that is, accessible to all nodes you plan to have as execution nodes for this external application. This is because different stages of your task could be run on different nodes. For example, the export process could run on a different node than the actual execution of the Bowtie script and the post processing. Thus, in a master-node setup, be it using grid or CLC execution nodes, having this shared temporary area eliminates the overhead of transferring the temporary files between nodes.