Referring to folders in WDL

Post author
Alex O

I'm writing a wdl file for a series of tools, one of which is hisat2. hisat2 requires a folder of hisat-index data, and uses all of the files in that folder. How do I reference this in the wdl file?

 

Thank you!

Comments

5 comments

  • Comment author
    Jason Cerrato

    Hi Alex,

    If you don't need to specify a directory and the tool can operate on the contents of the current working directory, you should be able to just localize the files then run the command, and the command will run on the files in the root directory. If you need to specify one, or you want to organize the files into a separate directory, you can simply run a mkdir command to create a directory and move the files into it, then run the tool on that directory.

    Does this make sense?

    Kind regards,

    Jason

    0
  • Comment author
    Karen Zheng

    Hi Jason,

    I have a similiar question. I need to specify a directory, say the files I need are in /Data in my google bucket, how do I move the files into a new directory? Thanks!

    0
  • Comment author
    Samantha (she/her)

    Hi Karen Zheng,

     

    You can move objects directly within the Google Cloud Console or by using the gsutil mv command. You can read more about how to use either of these methods in the following docs: https://cloud.google.com/storage/docs/renaming-copying-moving-objects#move and https://cloud.google.com/storage/docs/gsutil/commands/mv.

    Also, an important thing to note is how the objects are actually stored within Google Cloud Storage:

     
     
    Best,
    Samantha
     
     
    0
  • Comment author
    Karen Zheng

    Hi Samantha,

    Thanks for your help! I am not sure whether I actually need to move things in the first place, actually. I plan on using a library that takes several paths to directories as input, including the location of data, where the output should go, and where the parameters are located. Right now in my workspace Files, there are Data/, Output/, and Params/ subdirectories accordingly. Is it possible to just pass in these directory paths to the library as normal even though they are in a Google bucket?

     

    Thanks,

    Karen

    0
  • Comment author
    Samantha (she/her)

    Hi Karen Zheng,

     

    Yes, that should be possible for you to do. If you encounter any issues with this, please let us know.

     

    Best,

    Samantha

    0

Please sign in to leave a comment.