Output Prefixing

In some scenarios, it's helpful to modify the output prefixing reported by Cromwell. For instance, in the case of Cromwell on Azure, Cromwell mounts the storage location as a FUSE filesystem. This leads to Cromwell reporting the location of output files or logs like so:

/cromwell-execution/rnaseq_standard/<UUID>/call-multiqc/multiqc_results.tar.gz

In general, this location is not ammenable to quickly leveraging in another script to download the file. In this case, we have chosen to create the output_prefix configuration option that allows prefixing any output locations with a string. For instance, if the output prefix is azure://container-name, the reported output of the above will be

azure://container-name/cromwell-execution/rnaseq_standard/<UUID>/call-multiqc/multiqc_results.tar.gz

This string is much more amenable to copying and pasting. You can set this configuration option by running the following command.

oliver config set output_prefix "azure://container-name"