Merge branch 'patch-flagstat_dirs' into 'develop'
Patch flagstat dirs This fixes the recent update of `ouputDir` from `String` to `File`. There are some `apply` method that are overloaded with both `String` and `File`, causing the pipeline to spew out weird error messages. @p.j.van_t_hof ~ this is what was causing the weird error earlier. See merge request !101