Double Outputs

[AkiNikolaidis]

When a workflow is completed, some of the outputs are created twice.

For example the group_stability_matrix.npz is saved within workflow_output/group_stability_matrix and within workflow_output/basc_workflow_runner/basc/join_group_stability

Many other files are saved both in their own folders in workflow_output as well as within workflow_output/basc_workflow_runner/basc/