samples.json and dockerImages.json causing problems in Cromwell on GCP

[leipzig]

Hi. This is probably more a Cromwell problem than a biowdl problem but you should be aware that some of these "files in files" schemes in this pipeline seem to be triggering problems trying to "delocalize" them in the cloud. I don't think this pipeline would run on GCP (or Terra) as is.

I'm seeing errors that are a little different than in #74
"message": "Failed to evaluate 'dockerImages' (reason 1 of 1): Evaluating read_json(ConvertDockerTagsFile.json) failed: Failed to read_json(\"gs://pipeline-outputs/caper_out/RNAseq/cddd8308-d8af-49a9-a19d-1f9572210606/call-ConvertDockerTagsFile/dockerImages.json\") (reason 1 of 1): java.lang.IllegalArgumentException: Could not build the path \"gs://pipeline-outputs/caper_out/RNAseq/cddd8308-d8af-49a9-a19d-1f9572210606/call-ConvertDockerTagsFile/dockerImages.json\". It may refer to a filesystem not supported by this instance of Cromwell. Supported filesystems are: HTTP, LinuxFileSystem. Failures: \nHTTP: gs://pipeline-outputs/caper_out/RNAseq/cddd8308-d8af-49a9-a19d-1f9572210606/call-ConvertDockerTagsFile/dockerImages.json does not have an http or https scheme (IllegalArgumentException)\nLinuxFileSystem: Cannot build a local path from gs://pipeline-outputs/caper_out/RNAseq/cddd8308-d8af-49a9-a19d-1f9572210606/call-ConvertDockerTagsFile/dockerImages.json (RuntimeException)\n Please refer to the documentation for more information on how to configure filesystems: http://cromwell.readthedocs.io/en/develop/backends/HPC/#filesystems",

https://support.terra.bio/hc/en-us/community/posts/360071465631-write-lines-write-map-write-tsv-write-json-fail-when-run-in-a-workflow-rather-than-in-a-task