Update to support Cromwell tasks and structs dependencies via zip file

[TomGardner]

Cromwell supports imports from sub-directories tasks and structs via a zip file. This issue is for an enhancement to support this functionality.

Update to Dockerfile could be similar to: COPY dependencies.zip /wdl_runner

Update to wdl_runner.sh could be similar to: `

Execute the wdl_runner

python -u wdl_runner.py \ --wdl wf.wdl \ --workflow-inputs wf.inputs.json \ --working-dir "${WORKSPACE}" \ --workflow-options wf.options.json \ --workflow-dependencies dependencies.zip \ --output-dir "${OUTPUTS}"`

Update to wdl_runner.py (main) could be similar to: parser.add_argument('--workflow-dependencies', required=False, help='The workflow dependencies (ZIP) file')

And (run): `

Submit the job to the local Cromwell server

    (result, metadata) = self.driver.submit(self.args.wdl,
                                            self.args.workflow_inputs,
                                            self.args.workflow_options,
                                            self.args.workflow_dependencies)`

[hisplan]

Has this been implemented into wdl_runner?

[TomGardner]

Hi. Sorry I closed this by mistake. I don't know if this has been implemented yet. Re-opened.