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The file system I'm running on doesn't allow the creation of hard-links. Cromwell is trying to create hard-links to directories, and when that fails, it's copying them. Which is leading to disk quota errors.

Is there a way that I can simply tell cromwell "try soft links first"? Without creating a whole config file?

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  • $\begingroup$ Hi could you tell us what your disk quota is please? $\endgroup$
    – M__ ♦
    Commented Jul 18, 2020 at 2:58
  • $\begingroup$ @Michael 4.9 TB. Which my pipeline fills up shortly before it's supposed to finish $\endgroup$
    – Greg Dougherty
    Commented Jul 19, 2020 at 23:32
  • $\begingroup$ It is possible to set configuration values via the command line. I haven't tried this, though (and it will probably make you command pretty long...) $\endgroup$
    – DavyCats
    Commented Jul 31, 2020 at 10:03
  • $\begingroup$ @DavyCats we broke down and created a config file. Problem is that for some reason cromwell insists on creating "<dirname>.tmp" directories with complete copies of the working directory $\endgroup$
    – Greg Dougherty
    Commented Jul 31, 2020 at 17:19

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