cromwell file permission declined
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
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.
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
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!
Hi Sevgi Umur Reagh,
Can you provide the image you are using, and also share your method with svelasqu@broadinstitute.org?
Thanks,
Samantha
I think the problem is simply that in the code:
You left a space after the "\" character, so it is not interpreted as a line continuation.
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