Additional Crunch2 CWL User Guide updates
A few ideas (I can work on these, once we agree on the list of changes to be made):1. 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)"
- Registering a workflow with Workbench => "Use --create-template to register a CWL workflow" -- use "--create-workflow" instead?
- 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?
- Append "(Deprecated)" to both page titles?
- Do we want to add a page to work with container_requests and / or workflows here?
- 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?
#7 Updated by Radhika Chippada almost 5 years ago
@ 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)
- 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.
#8 Updated by Lucas Di Pentima almost 5 years ago
Some minor comments:
- could be renamed to
- 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
- could be renamed to
- Should CWL and UUID references be always in uppercase, as they’re acronyms?
Other than that, looks good to me.