I think this was a mistake in the merge since this is a perl variable not one to be passed to the workflow engine
Trying to fix a problem where aligned bams were included with unaligned bams as inputs to the bwa workflow when 'forcing' a realignment
I think it's better to have force override only those that have previous alignment rather than all the other situations since the latter approach means you get the same workflow running over and over again and I don't see a use case when we would want this.
Adding in an option to skip the upload of metadata to a GNOS repo for validation. This is useful for locations (like BioNimbus currently) where GNOS is offline or unavailable.
Adding in options to the decider to skip GNOS validation
Fixing help message
bug fix
This should be a lot faster on BioNimbus since the temp and destination share a filesystem. Rsync would require an actual timeconsuming copy operation
added GNOS Dowload