I have some code that tries to generate a table as a file and then send that file to a task. The code looks like this:
File? reheader_file = if reheader then write_map(as_map(zip(barcode, sample_ids))) else None
However, when I run the workflow in Terra I get an error like this:
Failed to evaluate 'reheader_file' (reason 1 of 1): Evaluating if (reheader) then write_map(as_map(zip(barcode, sample_ids))) else None failed: Failed to write_map(...) (reason 1 of 1): java.lang.IllegalArgumentException: Could not build the path "write_map_b4c827dcbcabc48a78ae8ece4b7e6d2d.tmp". It may refer to a filesystem not supported by this instance of Cromwell. Supported filesystems are: HTTP, Google Cloud Storage, DRS. Failures: HTTP: write_map_b4c827dcbcabc48a78ae8ece4b7e6d2d.tmp does not have an http or https scheme (IllegalArgumentException) Google Cloud Storage: Path "write_map_b4c827dcbcabc48a78ae8ece4b7e6d2d.tmp" does not have a gcs scheme (IllegalArgumentException) DRS: write_map_b4c827dcbcabc48a78ae8ece4b7e6d2d.tmp does not have a drs scheme. (IllegalArgumentException) Please refer to the documentation for more information on how to configure filesystems: http://cromwell.readthedocs.io/en/develop/backends/HPC/#filesystems
I get a sense that Cromwell on Terra is unable to serialize files. However, this is perfectly valid WDL code and it runs perfectly fine on my Cromwell instance running on my laptop. How am I supposed to work around this limitation?
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