Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

How to localise a directory with a symbolic link using Cromwell?

Hi there!

I'm new to both WDL and Cromwell. I'm trying to run a workflow and the main input is an Illumina run folder, which could be up to a Tb in size and have thousands of files. So I don't want it to be copied or hard-linked (which is almost the same in time) but to be soft-linked (only a soft-link to the directory). I changed the order in the localization option in the backend but even then I'm getting the following error:

Cannot localize directory with symbolic links

So, isn't this possible? Will I always have to hard-link the directories? This is not an option in my case due to performance issues. Everything is in the same shared file system, so I don't see the point in hard-linking. Also, if I call the same directory in different tasks, will it be hard-linked every time?

Thank you very much in advance!


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