Added modality passing to harmony pipeline

[ddemaeyer]

Changelog

... Describe your changes ...

Issue ticket number and link

Closes #xxxx (Replace xxxx with the GitHub issue number)

Checklist before requesting a review

• [x] I have performed a self-review of my code

• [ ] Conforms to the Contributor's guide

• Check the correct box. Does this PR contain:

  • [ ] Breaking changes
  • [ ] New functionality
  • [ ] Major changes
  • [ ] Minor changes
  • [x ] Bug fixes

• [ ] Proposed changes are described in the CHANGELOG.md

• [ ] CI tests succeed!

[rcannood]

I don't think this is correct. The modality argument should already be passed to move_obsm_to_obs through the workflowarguments:

  output_ch = input_ch
    | preprocessInputs("config": config)
    // ↓ this will prepare the incoming args to be passed to the move_obsm component
    | setWorkflowArguments(
      // ...
      move_obsm_to_obs_leiden: ["modality": "modality"]
    )
    // ↓ this fetches those args and puts it in the current data tuple
    | getWorkflowArguments(key: "move_obsm_to_obs_leiden")
    | move_obsm_to_obs.run(
        args: [ obsm_key: "leiden", output_compression: "gzip"],
        auto: [ publish: true ],
    )

As such, there shouldn't be a need for overriding it manually afterwards. In addition, this parameter will set modality to "modality".

What is the error message of the bug you're attempting to fix with this PR?

[DriesSchaumont]

Yes, this was already addressed in 113128e