Arvados

@ 6b2481ad in branch 10604-crunch2-user-guide

Run a pipeline using Workbench section:

• Rather than implementing those ideas listed under this item, per Peter's suggestion, updated the page to use bwa-mem.cwl so that it is the same one way or another.
  • In crunch2 only environments, where bwa-mem.cwl is a "workflow" instead of a "pipeline_template", the default values will not be populated due to issue #10576, but works as expected in qr1hi. Also, #10576 is on this sprint, so it's ok to update the user guide at this time with the expectation that the user guide steps will work as expected in 9tee4 as well pretty soon.

• Deleted crunch1only note from this page due to this.

• Updating the page required adding bwa-mem.cwl "pipeline template" to "Arvados tutorial public project" in qr1hi

user/cwl/cwl-runner.html -- Registering a workflow with Workbench => "Use --create-template to register a CWL workflow" -- use "--create-workflow" instead?

This was already done by Tom (when he made the change to --create-workflow == --create-template update)

topics/arv-copy.html

• Added a note at the top of the page saying arv-copy for workflows is not yet implemented

Working on the command line

• Made several include files from the "Using Common Workflow Language" page and using these shared include files added a "Running an Arvados workflow" page

Develop an Arvados pipeline

• Using the includes from the "Using Common Workflow Language" page, added a new "Writing a CWL workflow" page

Append "(Deprecated)" to page titles ...

Since we do not yet have crunch2 working in qr1hi, it is not the right time to add "(Deprecated)" to page titles. For now the note within the page with "crunch1 deprecated" note will suffice. We can add this to the page titles when are supporting Crunch2 in qr1hi environment.

Some minor comments:

• doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid file:
  • could be renamed to tutorial-workflow-workbench.html.textile.liquid for consistency?
  • Maybe if we don’t want to break backlinks, we can leave the old file with a link referring to the new one? Or a http redirection?
  • Typo: pupulated
• doc/_includes/_arvados_cwl_runner.liquid & doc/user/cwl/cwl-runner.html.textile.liquid files:
  • Should CWL and UUID references be always in uppercase, as they’re acronyms?

Other than that, looks good to me.

@ c494f4c3

doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid file

Renamed this file as tutorial-workflow-workbench.html.textile.liquid

CWL and UUID in uppercase

Updated to uppercase

Thanks.