Expose Snakemake generation of APE to RestfulAPE

[eladrion]

Pull Request Overview

This PR updates RestAPE by depending on APE 2.6.1 and exposing Snakemake files generated by APE

Related Issue

Changes Introduced

RestAPE now triggers the generation of Snakemake files. Also, the Snakemake files are added to the workflow ZIP file
and the Snakemake files are retrievable separately

How Has This Been Tested?

• Local testing with test suite.
• Local testing using cURL, i.e. generating solutions, calling POST method snakemake
• Tested with updated Workflomics-frontend on private institutional instance at UP

Checklist

• I have referenced a related issue.
• I have followed the project’s style guidelines.
• My changes include tests, if applicable.
• All tests pass locally.
• I have added myself to the CITATION.cff file, if not already present.

[vedran-kasalica]

Thanks @eladrion, the changes look good, and it's nice that you also improved the JavaDocs in the process!

The only observation (similar to the one in workflomics PR #111 is that it might be rare that a user wants a zip file that includes both cwl and snakemake files. Maybe the request can have parameters that determine what is returned. Or zip could include folders based on the availability, e.g., if 0 cwl files were requested in the configuration file the zip should not include the cwl folder.

[eladrion]

Hi @vedran-kasalica, I like the idea of optional subfolders depending on requested and existing language specific outputs. I will implement this as a separate PR and it will also become part of v1.1.

[vedran-kasalica]

Thanks @eladrion, sounds great! Feel free to merge this PR in that case

[eladrion]

Hi @vedran-kasalica. Issue created for subfolders. Merging now.