order of step

[aliceminotto]

To solve this: how to ask the user for the order of the steps to perform in agave app?

1. i could ask for parameter: [ ... { "id": "step1", "value": {"type":"enumeration" .......}}. BUT:
   • it gets longer
   • i can't enforce this to be bound to the other options given
   • what if this is not given but the parameter for one step are, have a default order? what's the default order?
2. drop everything and rewrite the app so that for each step a string is given by the user (i can add a validator), then i make the user select a number. BUT:
   • i can't enforce the user do give number that makes sense4 in agave (like ordered, no jumps, no duplicated numbers)
3. i could do like the previous but asking for the step (so up to # of possible steps), ask for a step to perform between enumValue with the possible step, and then ask for the string. Problems:
   • i can't enforce not to choose duplicated steps
   • validator can't be expressed in the app as i don't know in advance which one is the step chose, would have to be done in wrapper
     (I think in the GUI this would come up as the most user friendly)

Additional problem: in ILLUMINACLIP a file is needed, so one more file has to asked no matter what in the app. That may not make sense.

4. I could also make the user write the whole command by end. There's no validation at this point, but it may not (or may?) be more confusing for user that know trimmomatic. The app and its user interface would be very compact on the plus side. We may have more failures, but I'm not sure how many could be avoided with the previous methods.

(check existing apps in the DE to see how they deal with this)

[aliceminotto]

most of the trimmomatics apps seem not to care about the order (nor they say anywhere what's their default!!!) and work as the current draft (define each parameter).
One app doesn't define the order and to be more compact gives enumeration to the different steps with (none) and a set of prechosen parameters. This solve the validation problem but it's not very flexible + there's no ordering of the step again.
The programmable app takes an additional input file where the user has to type down by themselves the options (and so can define the order). this is basically as option 4 above. (note that this one is not the one in the list of most used apps)