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.
Soft-link localization not working
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
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?