Positional inputs

[mqualls]

How can I set up a pipeline to run stage1 on input1 and stage2 on input2 (with a stage3 that takes both the prior outputs as input)?  I'd like the behavior to be governed by positional order. Swapping the order of the two inputs would be a valid, but different, operation.

The files are of the same type, so there's not a convenient way to differentiate using extensions. Using $input2 in a stage makes it expect two inputs internal to that stage alone.

Passing names as variables loses the fact that these are input files, so there's no dependency tracking.

[Simon Sadedin]

There are a few different ways to do it that implicitly get the second input to be used in the second stage, but if positional order is really how you want to drive the recognition of the inputs, I actually suggest adding an init stage that identifies them by name using branch variables.

Here's a simple example:

init = {

    branch.first = input1

    branch.second = input2

}

hello = {

    from(first) {

        exec """

            cp -v $input $output

        """

    }

}

world = {

    from(second) {

        exec """

            cp -v $input $output

        """

    }

}

run {

    init + hello + world

}

Here I just called them 'first' and 'second' but obviously you can name them something meaningful in terms of what they actually represent.

Hope this helps!

Simon

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[Morgan Qualls]

Thanks, that should do nicely.

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