Arvados

• "This section assumes the legacy Jobs API is available. Some newer installations have already disabled the Jobs API in favor of the Containers API. On those sites, the details will be slightly different and the example pipelines might not be available."

• "This section assumes the legacy Jobs API is available. Some newer installations have already disabled the Jobs API in favor of the Containers API. On newer installations, use Common Workflow Language instead.

• "This section assumes the legacy Jobs API is available. Some newer installations have already disabled the Jobs API in favor of the Containers API. On those sites, the features described here are not yet implemented."

A few ideas (I can work on these, once we agree on the list of changes to be made):

Run a pipeline using Workbench section:

• Rename as "Using Crunch" or something like that

• Move "Introduction to Crunch" from "Develop an Arvados Pipeline" as the first item in this section

• Add a new page "Running a workflow using Workbench" after "Accessing workbench". This would of course need adding a tutorial workflow to qr1hi and authoring this page etc

• Rename "Running a pipeline using workbench" as "Running a pipeline using workbench (Deprecated)"

user/tutorials/tutorial-keep.html

• diagram under "Locate your collection in Workbench" has wrong tab title for pipelines tab (and the other diagram too, but it is not too apparent here)

topics/arv-copy.html

• How to copy a pipeline template => Do we need to add any notes here about workflows? Otherwise, add a "How to copy a workflow" section?

user/cwl/cwl-runner.html

• Registering a workflow with Workbench => "Use --create-template to register a CWL workflow" -- use "--create-workflow" instead?

Working on the command line

• Append "(Deprecated)" to both page titles?

• Do we want to add a page to work with container_requests and / or workflows here?

Develop an Arvados pipeline

• Rename it as "Develop an Arvados pipeline (Deprecated)" ?

• This would need moving a couple pages.
  • Move "Introduction to Crunch" to the top of the list as noted in the first comment
  • Add a new "Docker" section and move "Customizing Crunch environment using Docker" into it?

Tom: please go ahead and merge 10499-cwl-crunch2-docs branch into master. I do not see any objectionable issues with your updates. Thanks.