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My recommended approach is to define BOTH the root directories of data and PGE directories you need for executing PGEs defined in either your tasks.xml file, or within a .bashrc file. Next, create derived environment variables for all your specific Windows PGE needs within your PGE. This way, the Linux and Windows environment variables are passed to your batchstubs through metadata automatically. 

Example implementation to look at:

Directory containing Linux/Windows configured PGE’s: https://github.com/EDRN/labcas-pipelines/tree/master/backend/workflows/proteome-pge/src/main/resources/config/tabblab

Example Win PGE file: https://github.com/EDRN/labcas-pipelines/blob/master/backend/workflows/proteome-pge/src/main/resources/config/tabblab/proteome-preprocessing.tabblab.pgeconfig.xml

Example .bashrc file (linux): https://github.com/EDRN/labcas-pipelines/blob/44871c37cf03d3484265eaacb8843ec3816e6546/backend/linux/config/src/main/conf/.bashrc

Example .bashrc file (win): https://github.com/EDRN/labcas-pipelines/blob/6338fd6a61f136ee08c725b08d8f828488b60702/backend/win/config/src/main/conf/.bashrc

Workflow Manager tasks.xml file (search for ProteomePreprocessingTabbLab): https://github.com/EDRN/labcas-pipelines/blob/master/backend/linux/workflow/src/main/conf/policy/proteomics-pipeline/tasks.xml