fix dockstore: add empty.json file and update .dockstore.yml with absolute paths to it

[kapsakcj]

This PR closes #344

🗑️ This dev branch should be deleted after merging to main.

:brain: Aim, Context and Functionality

:hammer_and_wrench: Impacted Workflows/Tasks & Changes Being Made

This will affect the behavior of the workflow(s) even if users don’t change any workflow inputs relative to the last version : Yes/No

Running this workflow on different occasions could result in different results, e.g. due to use of a live database, "latest" docker image, or stochastic data processing : Yes/No

:clipboard: Workflow/Task Step Changes

🔄 Data Processing

Docker/software or software versions changed:

Databases or database versions changed:

Data processing/commands changed:

File processing changed:

Compute resources changed:

➡️ Inputs

⬅️ Outputs

:test_tube: Testing

Test Dataset

Commandline Testing with MiniWDL or Cromwell (optional)

Terra Testing

Suggested Scenarios for Reviewer to Test

Theiagen Version Release Testing (optional)

:microscope: Final Developer Checklist

• [ ] The workflow/task has been tested locally and results, including file contents, are as anticipated
• [ ] The workflow/task has been tested on Terra and results, including file contents, are as anticipated
• [ ] The CI/CD has been adjusted and tests are passing (to be completed by Theiagen developer)
• [ ] Code changes follow the style guide

🎯 Reviewer Checklist

• [ ] All impacted workflows/tasks have been tested on Terra with a different dataset than used for development
• [ ] All reviewer-suggested scenarios have been tested and any additional
• [ ] All changed results have been confirmed to be accurate
• [ ] All workflows/tasks impacted by change/s have been tested using a standard validation dataset to ensure no unintended change of functionality
• [ ] All code adheres to the style guide
• [ ] MD5 sums have been updated
• [ ] The PR author has addressed all comments

🗂️ Associated Documentation (to be completed by Theiagen developer)

• [ ] Relevant documentation on the Public Health Resources "PHB Main" has been updated
• [ ] Workflow diagrams have been updated to reflect changes

[kapsakcj]

This seems to have resolved the dockstore syncing issue. We can see successful GH app sync logs here:

and new development branches, like this one cjk-dockstore-updates are appearing in the list of versions for TheiaCov_Illumina_PE:

I think we need to get this PR merged ASAP and then have others merge main branch back into their dev branches so changes propagate to new dev branches so the error goes away

[cimendes]

should we create the empty.json file in tests/inputs/ (given that the folder exists, maybe the file should exist too? Of not, idk if I prefer the solution with just /empty.json as not to confuse anyone :) @kapsakcj thank you for being so speedy!