One of our collaborators from ROCHE downloads data from Synapse to use in cBioPortal. Currently, when importing files into cBioPortal, it detects all the files that are downloaded in the folders and since the MANIFEST file is not a valid filetype, the user cannot import the study without failing.
I think this is something that should probably be fixed on the cBioPortal side, and the easy solution is to simply remove the MANIFEST files. That being said, was wondering if this flag would be worth having.
It seems reasonable and an easy enough fix. I had a similar comment about the table query file generated from interfering with a workflow so it may make sense to suppress that with a similar argument as part of resolving this issue.