Cromwell cannot delocalize Array[Array[File]]

[archanaraja]

Hi ,
Im running the GATK warp joint genotyping pipeline cromwell on GCP backend . The pipeline fails because cromwell cannot localize files with certain data types like Array[Array[String]]

This issue was reported on the terra website too and the workaround was to write a task to read file into an array, I have performed the workaround but are there plans to fix this issue in any upcoming releases.

Cromwell version tested : 85

Are you seeing something that looks like a bug? Please attach as much information as possible.
"Failed to evaluate 'sample_name_map_lines' (reason 1 of 1): Evaluating read_tsv(sample_name_map) failed: Failed to read_tsv(\"gs://wgs/test/sample_map.txt\") (reason 1 of 1): java.lang.IllegalArgumentException: Could not build the path \"gs://wgs/test/sample_map.txt\". It may refer to a filesystem not supported by this instance of Cromwell. Supported filesystems are: HTTP, LinuxFileSystem. Failures: \nHTTP: gs://wgs/test/sample_map.txt does not have an http or https scheme (IllegalArgumentException)\nLinuxFileSystem: Cannot build a local path from gs://wgs/test/sample_map.txt (RuntimeException)\n Please refer to the documentation for more information on how to configure filesystems: http://cromwell.readthedocs.io/en/develop/backends/HPC/#filesystems"

Which backend are you running?
GCP

Link to the workflow if possible
https://github.com/broadinstitute/warp/blob/develop/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl