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v0.9.0: New component: CommandToParams, to read stdout from a command into a stream of parameters

@samuell samuell released this
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Often in workflows, we need to generate a list of parameters commandline to drive workflows. For example if we have a list of target proteins for which we want to create predictive models for, for drug molecules, out of a large combined dataset. Optimally this should be doable with any shell command, so that it can be generated based on some existing data. We recently realized that there is not really an easy way to do this in SciPipe currently. Until now.

Now there is the new CommandToParams component.

We will update with docs shortly, but in the meanwhile, the test contains a small (quite dumb) mini example of how to use it.

Note: We have plans to create a more integrated solution for reading data into parameter streams, so that this can be done in the normal shell commands created with workflow.NewProc(), but this dedicated component is created to serve the basic need for this functionality while we get that in place.

Small breaking change: components.{FileReader -> FileToParamsReader}

This release also renames the FileReader component to FileToParamsReader, as we realized that it was not really functioning properly in its previous role, where the inclusion of line breaks was causing troubles. It is now properly unit tested to function for reading individual rows in files into a stream of parameter values to send on the parameter ports of other processes.

This small breaking change means we're ticking the (still pre 1.0) version from 0.8.x to 0.9.x.