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Is it possible to specify workspace attribute as array of arrays?

I want to pass two-dimensional array to wdl script.
Is it possible to specify it as workspace attribute or as field of entity?

Thank you.

Answers

  • RuchiRuchi Member, Broadie, Moderator, Dev admin

    Hey @NLukashina,

    I tried testing this and it seems like when you try to use an attribute of the type Array[Array[_]] as an input to your WDL from an entity/workspace, there are coercion issues. My recommendation is that you coerce the content inside your array of arrays into a tsv, add that file as an attribute to a workspace or entity, and then use the function read_tsv() inside your wdl script to coerce the contents of that file into an array of arrays. Meanwhile, I've filed an issue on our end to look into this further.

  • RuchiRuchi Member, Broadie, Moderator, Dev admin

    UPDATE: @NLukashina I tested extracting array of array types from workspace/entity attributes today to use as inputs in a WDL script and it seems to be working! There was a recent release and that seems to have fixed the issue. Let us know if you experience any issues with writing/reading array of arrays to/from entity/workspace attributes. Thanks!

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