For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues on Github.
Using imports and workflowDependencies with wdl_runner.sh and gcloud
it looks like Cromwell wrapper
as obtained from
cannot handle workflowDependencies and therefore cannot be used to launch the wdl script in
Is that correct?
I could discard the imports and flatten the wdl, but it would be much better to keep the original structure. And it would be nice if I -for now- could keep on using the wrapper, without digging deeper into Cromwell :-)
My current gcloud command is based on the example below, so I guess an extra parameter would be needed to specify the five-dollar-genome-analysis-pipeline/tasks_pipelines folder with the imports?
alpha genomics pipelines run \
--pipeline-file wdl_pipeline.yaml \
--zones us-central1-f \
--inputs-from-file WDL=test-wdl/ga4ghMd5.wdl \
--inputs-from-file WORKFLOW_INPUTS=test-wdl/ga4ghMd5.inputs.json \
--inputs-from-file WORKFLOW_OPTIONS=test-wdl/basic.papi.us.options.json \
--inputs WORKSPACE=gs://YOUR-BUCKET/wdl_runner/work \
--inputs OUTPUTS=gs://YOUR-BUCKET/wdl_runner/output \
Thanks for your help,