Using a config file as input to workflow to set workflow parameters and other tool settings

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.

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These can have pre-set content. But if the users need to adjust these, then you might want to create copies/variations of the workflow for specific genomes or analysis projects.

There isn’t a way to use a config file that I know of through the web interface, but it might be possible when running a workflow through the API. You’ll need to test that out as a potential solution – IF your users are able/willing to run workflows that way. API help:

If you want to make a request to the developers about this, two choices:


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