How can I use a config file (yaml, json, etc) as an input to the workflow, to set workflow parameters and tool settings?
For example, set reference genome, max insert size for an aligner, min length after trimming for the adapter trimmer, etc - all in 1 file.
We currently use multiple workflow parameters such as ${max insert size}, etc. There is also a newer method, using Simple inputs used for workflow logic. Apparently, both of these methods require the user to type in or select 1 parameter at a time. The config file sets multiple parameters per config.
For many of our users, this would be more robust and faster than selecting these every time the workflow is run. The config file also provides a nice record of the most frequently changed parameters/settings, for record keeping and for debugging.
In most cases, the user changes only a minority of the lines (if any) in a file such as this.