Use annotations on protocols in the demux and mask/align step to set some program parameters
|Reported by:||Nicklas Nordborg||Owned by:||Nicklas Nordborg|
Some program parameters for picard, bowtie, tophat, etc. are currently configured in the reggie-ogs-hosts.xml file. It would be nice to define protocol annotations for some of those parameters. In the gui it is already possible to select a protocol, but we would need to add checks that parameters that are required are set.
We have to think about which of the parameters should be moved to annotations and which that should remain in the configuration file. Some parameters could also be annotations on the software items or have fallbacks to default values.