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Using fofn files in docker

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3 comments

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    Jason

    Hi Matthias,

    Thanks for writing in. We'll take a look at your issue and get back to you as soon as we can!

    Kind regards,

    Jason

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    Jason

    Hi Matthias,

    Would you be able to create a .list file in your first task that gets fed into your next task as input? Here is a WDL that may give you an idea of how to write it into your WDL: https://portal.firecloud.org/#methods/bshifaw/make_fofn/3/wdl

    Are you feeding the files from the fofn as input to the second task, or streaming those files in? If the solution above doesn't work for you I would love to get more details about the relationship between the two tasks, the fofn, and the actual files included in that list. If you would like me to take a closer look at your WDL, please share it with jcerrato@broadinstitute.org and I'll be happy to take a closer look.

    Kind regards,

    Jason

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    Matthias De Smet

    Hi Jason,

     

    Thanks for the reply!

    Might I refer to a github issue for more info? https://github.com/openwdl/wdl/issues/452 

    I'll also shoot you an e-mail with the workflow, perhaps it might be more clear then.

     

    Thanks again

    Matthias

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