Files aren't being localized to the work directory when they are workflow inputs.

[claymcleod]

When using a File as the input to a workflow in wdl, it doesn't appear that the files are properly being localized to the work directory. It seems as though the files are localized if they aren't inputs to the workflow.

For example,

version 1.2

task count_lines {
    input {
        File file
    }

    command <<<
      wc -l ~{file}
    >>>
}

workflow run {
    input {
        File file
    }

    call count_lines { input: file }
}

This will fail because file is not localized to the count_lines working directory.