@jmchilton there are a few tailing tests, especially the simple sub-workflow test is failing.

• subworkflows are not expandable in the run workflow view
• the name of the subwokflow in toolbox is not clickable
• I was not able to do much with workflow inputs. There was no option to combine a input with a tool/subworkflow.

Midterm ideas:
I don't think listing workflows in the toolbar works for a large set of workflows. I imagine a overlay with a list of workflow and previews that you can drag and drop into your current workflow. This preview would be also nice to have as information (hover?) for the subworkflow module.

It would be nice to switch quickly to a subworkflow and adjust settings.

Docker Image to test:

docker run -p 8080:80 -e GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES=True -i -t bgruening/galaxy-stable:jmc_workflow

@bgruening Thanks for the initial review and Docker image.

• Pushed out 7c459cb - which I'll eventually rebase back into the subworkflow commit (03befc6) which should fix the 4 new failing tests that aren't also failing in Improved validation of tools during workflow execution. #1302. Still no clue why those existing 6 failures occur on Jenkins - they don't fail locally for me. Update: All failing tests have been fixed the PR rebased.
• "subworkflows are not expandable in the run workflow view" The run workflow view is on its death bed (Run workflow form #1249) so I don't intend to do any polish there.
• "the name of the subwokflow in toolbox is not clickable" There is a little link icon next to the workflow to link the workflow in as a subworkflow. If you look at the comments in the editor mako I've already started working on a second icon for copying the clicked workflow into the workflow being edited (add all nodes at once). There will be use cases for both of these operations so I was just thinking of having separate icons instead of favoring either operation as "what" occurs when the title is clicked. I'll update PR with pictures of this if I get the second operation implemented before this is merged. Update: The PR has been updated and there are now two icons which do different things.
• "I was not able to do much with workflow inputs. There was no option to combine a input with a tool/subworkflow." Yes, like pause steps - these require a significant overhaul to the UI to be useful from Galaxy's UI so it is labelled as "experimental" and not enabled by default. That said - they are fully functional from an API standpoint and integrated into the format 2 workflow language. An example that just defines a data and a text input and runs the random lines tool with the supplied input as the seed would be:

class: GalaxyWorkflow
inputs:
  - label: data_input
    type: data
  - label: text_input
    type: text
steps:
- label: randomlines
  tool_id: random_lines1
  state:
    num_lines: 1
    input:
      $link: data_input
    seed_source:
      seed_source_selector: set_seed
      seed:
        $link: text_input
      __current_case__: 1

Your midterm ideas are excellent. I think many of them would be more competently implemented by @guerler. Workflow previews seem on the surface challenging - maybe just exposing the description and annotation information would be more feasible. Regardless, I'll create an issue for refinements to workflow nesting.

Updated PR with bug fixes (same fixes that fixed #1302) and adding the "copy into" functionality in addition to the "link into" functionality already included in the PR. Updated description to include a screenshot distinguishing these.

Image is updated:

    docker run -p 8080:80 -i -t bgruening/galaxy-stable:jmc_workflow

• "subworkflows are not expandable in the run workflow view" The run workflow view is on its death bed (Run workflow form #1249) so I don't intend to do any polish there.

Fair enough.

• "the name of the subwokflow in toolbox is not clickable" There is a little link icon next to the workflow to link the workflow in as a subworkflow. If you look at the comments in the editor mako I've already started working on a second icon for copying the clicked workflow into the workflow being edited (add all nodes at once). There will be use cases for both of these operations so I was just thinking of having separate icons instead of favoring either operation as "what" occurs when the title is clicked. I'll update PR with pictures of this if I get the second operation implemented before this is merged.

I saw this small symbol and everything worked great. Maybe I missed that to say, I'm too excited!!!
I still think that a user expect that the link is click able and not just the symbols to the right. This is a usability issue and does probably not belong into this PR.
What about a single link that embedds the subworkflow as one item and in the header of this item you offer the expandable option?

• "I was not able to do much with workflow inputs. There was no option to combine a input with a tool/subworkflow." Yes, like pause steps - these require a significant overhaul to the UI to be useful from Galaxy's UI so it is labelled as "experimental" and not enabled by default. That said - they are fully functional from an API standpoint and integrated into the format 2 workflow language. An example that just defines a data and a text input and runs the random lines tool with the supplied input as the seed would be:

Awesome!

+1 from my site if the usability issues can be fixed in this release cycle.

@jmchilton one question regarding your Input Parameters. Is this framework flexible enough to enable text files as parameter inputs? Use case: Calculate inner mate distance of paired end reads and use this output as integer input parameter in a mapping tool.

@bgruening Not yet, CWL has this concept of expression tools and I have been working on a pure Galaxy (you know with XML 😄) analog common-workflow-lab@96f6550 that should enable something like this. Needs some work still, I am hacking on it though.

Awesome you rock! Just wanted to make sure we can tackle this use case as well in your implementation/design ... but sure you thought of everything! I should have known better!

Thanks @jmchilton !!! Really terrific!!!!!! After some tests on the Docker image through our genocloud instance http://cloud-87.genouest.org/, it seems to work. Just few remarks. Is it possible to see the name of the subworkflow on the workflow editor ? We have encountered some save / rename issues who seem to be more related to communication lag between docker image / cloud machine / host machine than to new workflow functionalities....

Now rebased for #1322 and #1323.

I'll work on placing some information about the original workflow in for @yvanlebras.

Does anybody agree strongly with @bgruening about clicking the workflows? I feel like I prefer the current setup with two icons over this suggestion.

Does anybody agree strongly with @bgruening about clicking the workflows? I feel like I prefer the current setup with two icons over this suggestion.

Not an usability expert, but I think that the current setup is ok because the workflow name is not underlined.

@nsoranzo Am I going to get a line-by-line 🐦 👀 critique of this or is it too big? Is there some sort of API for requesting such reviews 😄?

@jmchilton 😆 I'm going on holiday in 24h, I doubt I'll have time to review any big PR for the next 20 days, sorry!

@nsoranzo We pay you too much to take 20 days off - GET BACK TO WORK 🐦 👀!

I know a few different people who care about workflows have at least looked at and thought about the input parameter stuff and had at worst neutral comments - so I am going to go ahead and merge those database migrations.

Picture of updated UI by @guerler that allows clicking on the workflows common-workflow-lab#13.

@guerler Is that the last of your changes, if you are read to merge I can rebase.

TS tests run fails at

File "lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py", line 28, in <module>
    Column( "parameter_value", JSONType ),
NameError: name 'JSONType' is not defined

@martenson should be fixed by c04899a. This branch is an absolute mess, but @guerler is working on some stuff still so I don't want to rebase quite yet.

Old messy history backed up here https://github.com/jmchilton/galaxy/tree/subworkflow_prerebase_1, I've rebased on top of the latest dev and this is now a clean history with one database migration.

@yvanlebras The subworkflow name is shown now in the workflow editor and can be edited.

As usual there are many more good follow up suggestions but this looks like a great step towards subworkflows to me 👍

@guerler thanks for the merge and thanks for all the enhancements!