Currently the "Log in with Google" button redirects you to a "Page not found." Our forum vendors have implemented a fix, and now we are just waiting on a patch to be released. In the meantime, while on the "Page not found" you can edit the URL to delete the second gatk, firecloud, or wdl (depending on what subforum you are acessing).
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,