Wrapping R scripts in WDL

Anton Kovalsky

This article provides some resources for those interested in running R scripts within their WDL code. 

The video below explains the steps of creating Docker files with the necessary dependencies for your R scripts, and how to run those R scripts from inside of a WDL script:

 

 

You can download the slides and samples of scripts from the above presentation here. Stay tuned as we continue to add resources and instructions to this article!

 

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Comments

1 comment

  • Comment author
    smk_84

    So is the r script needed to be run inside the wdl using 

    ```

    command <<<

    R ~{scriptname_rscript} --no-save --args ~{argname1} ~{argname2}

    >>>
    ```

    Why can't we run it using Rscript instead?

    ```

    command <<<

    Rscript ~{scriptname_rscript} ~{argname1} ~{argname2}

    >>>
    ```

     

     

     

    0

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