cromwell file permission declined

Post author
Sevgi Umur Reagh

Hello,

 

Im running a workflow on Terra using a image hosted on gcr. My image has the scripts built in, and has symlinks (/usr/local/bin/)

my code looks like(not letting me format here):

 

version 1.0

workflow test {

input {
File inputFile
String image
}

call sample_sheet { input:
inputFile= inputFile,
image = image,
}
}

task sample_sheet {
input {
File inputFile
String image
}

command {

python /usr/local/bin/sample_sheet \
"${inputFile}"

}
}

I am getting an error as below:

/cromwell_root/script: line 24: /cromwell_root/fc-90656418-1508-427d-bd2d-091f50c98dee/input_file.txt: Permission denied

Comments

4 comments

  • Comment author
    Samantha (she/her)

    Hi Sevgi Umur Reagh,

     

    Thanks for reaching out. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

    1. Add GROUP_FireCloud-Support@firecloud.org to the User email field and press enter on your keyboard.
    2. Click Save.

     

    Let us know the workspace name, as well as the relevant submission and workflow IDs. We’ll be happy to take a closer look as soon as we can.

     

    Best,

    Samantha

    0
  • Comment author
    Sevgi Umur Reagh

    Hi Samantha, 

     

    Thank you for your response. the work space name is honeycomb-billing/Hive_Terra, the workflow is task_wdl v.30, 0c9fba57-5b9f-4739-b0b7-f27ef0a8507d

    this is the latest submission where I've tried to re-produce the same error.

     

    Thanks!

     

    0
  • Comment author
    Samantha (she/her)

    Hi Sevgi Umur Reagh,

     

    Can you provide the image you are using, and also share your method with svelasqu@broadinstitute.org?

     

    Thanks,

    Samantha

    0
  • Comment author
    Giulio Genovese

    I think the problem is simply that in the code:

    python /usr/local/bin/sample_sheet \ 
    "${inputFile}"

    You left a space after the "\" character, so it is not interpreted as a line continuation.

    0

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