We've moved!
For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues on Github.

Soft-link localization not working

dario_romagnolidario_romagnoli Member
edited November 2018 in Ask the Cromwell + WDL Team

I'm running the gatk-somatic-snvs-indels workflow locally and all resources files reside on a different file-system from the one where I' running the analysis. Since hard-linking can't be performed but I don't want all the files to be copied I set localization: ["soft-link"] in my cromwell.conf file and passed it to cromwell with
java -Dconfig.file=/resources/tools/cromwell/cromwell.conf -jar /resources/tools/cromwell/cromwell-36.jar run.
The problem is that cromwell completely ignores the configuration emitting the warning [warn] Localization via hard link has failed and proceeding to copy the files thus quickly filling up the disk. What might be the problem?



Sign In or Register to comment.