Config restructure

[jfy133]

Closes https://github.com/nf-core/mag/issues/501

Proposal table: https://github.com/nf-core/mag/issues/501#issuecomment-2139584648

• [x] test (separate run)
• [x] test_single_end
• [x] test_alternatives
• [ ] test_preassembly_binrefine -> might be problematic due to very slow download of CheckM (Aria2)/Genomad/Gunc databases...
  • [ ] https://portal.nersc.gov/genomad/data/genomad_db_v1.7.tar.gz
    • Maybe replace with: https://github.com/apcamargo/genomad/issues/104
    • Which was kindly uploaded to Zenodo: 10.5281/zenodo.11945947 (make sure to thank!)
  • [ ] METAEUK Various internal (11 minutes locally) -> replace with FASTA file of the bacteria (/home/james/Downloads/ncbi_dataset/ncbi_dataset/data/GCA_000009925.1/protein.faa) -> This is causing my laptop to crash when mmseqs tries building, consider trying swissprot again? -> CURRENTLY PUSHED MODULE YEAST, SHOULD MOVE TO MAG BRANCH IF SO
• [ ] test_hybrid_rm
• [x] test_nothing
• [ ] test_extras
• [ ] test_bigdb
• [x] test_full

PR checklist

• [ ] 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 pipeline conventions in the contribution docs
• [ ] If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
• [ ] Make sure your code lints (nf-core lint).
• [ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• [ ] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• [ ] Usage Documentation in docs/usage.md is updated.
• [ ] Output Documentation in docs/output.md is updated.
• [ ] CHANGELOG.md is updated.
• [ ] README.md is updated (including new tool citations and authors/contributors).