This has been fixed for HAMLET in d94a939f1a9effd34989dc1d6e37e8155e9db5ae. File paths with spaces are not supported in the fusion module as of yet, since STAR-Fusion cannot handle files with spaces.
In HAMLET itself, the fusion module never gets file paths with spaces, since it gets the output from the QC module, which does not contain spaces.
This has been fixed for HAMLET in d94a939f1a9effd34989dc1d6e37e8155e9db5ae. File paths with spaces are not supported in the fusion module as of yet, since STAR-Fusion cannot handle files with spaces.
In HAMLET itself, the fusion module never gets file paths with spaces, since it gets the output from the QC module, which does not contain spaces.