Port gget/gget to nf-test and update

[famosab]

PR checklist

Closes #7588

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[famosab]

For search_json_human

    12:44:09 - INFO - Fetching results from database: homo_sapiens_core_114_38
    Traceback (most recent call last):
      File "/opt/conda/bin/gget", line 10, in <module>
        sys.exit(main())
                 ~~~~^^
      File "/opt/conda/lib/python3.13/site-packages/gget/main.py", line 2895, in main
        gget_results = search(
            sw_clean_final,
        ...<7 lines>...
            verbose=args.quiet,
        )
      File "/opt/conda/lib/python3.13/site-packages/gget/gget_search.py", line 233, in search
        raise RuntimeError(
            f"The Ensembl server returned the following error: {str(last_exception)}"
        )
    RuntimeError: The Ensembl server returned the following error: 2003 (HY000): Can't connect to MySQL server on 'mysql-eg-publicsql.ebi.ac.uk:5316' (111)

[famosab]

@adamrtalbot

[SPPearce]

Well I fixed the singularity issue, but now for some reason one of the tests gives output in conda but not in docker/singularity?

[SPPearce]

The muscle test silently fails for docker/singularity with:
chmod: changing permissions of '/opt/conda/lib/python3.13/site-packages/gget/bins/Linux/muscle': Operation not permitted present in the .command.err.

[LouisLeNezet]

Do you have anyworking nf-test with a file in input instead of a empty tuple ?

[LouisLeNezet]

What is this "files" output ?
There aren't generated in the nf-test

[LouisLeNezet]

Do we still need to explain that this is a meta map ?

[LouisLeNezet]

Why are they commented out ?

[LouisLeNezet]

I would have grouped the different stub test together, but not a deal breaker.