Hi again,
Looking at the WDL log, I saw that each time used a File input as `File("dx://file-id")` there was an hidden call to `dx download`. So am I right to say that each use of `File` in an input will always result in a call to `dx download` ?
( So my guess is sometimes, it's better to use an input=`String file-id` and use `dx download` within the `command` section if you're not sure whether the file will be used in the script )
I do not think that dx download would work in WDL too since the Docker might not have dx-toolkit installed even though the instance always have dx-toolkit.
I was recommended that the best practice is to sort out the input using the variable that contain file path rather than trying to download specific files to specific location. Usually, in the WDL ,the input goes to some temp folder that can't be predicted ahead of time. Your idea sounds legit , but I'm not sure if that would work out well with the system. For example, I'm not sure if Docker would have permission to interact with project and handle mounting properly. I guess it needs experiment or other community members could chime in.
Comments
1 comment
There is a way to do use the file without downloading them. See: https://youtu.be/vyzYChm0e1g?t=519
I do not think that dx download would work in WDL too since the Docker might not have dx-toolkit installed even though the instance always have dx-toolkit.
I was recommended that the best practice is to sort out the input using the variable that contain file path rather than trying to download specific files to specific location. Usually, in the WDL ,the input goes to some temp folder that can't be predicted ahead of time. Your idea sounds legit , but I'm not sure if that would work out well with the system. For example, I'm not sure if Docker would have permission to interact with project and handle mounting properly. I guess it needs experiment or other community members could chime in.
Please sign in to leave a comment.