feat!(prepro, config): assign segment with nextclade sort

[anna-parker]

resolves #4847

Screenshot

Builds on #4821

You can use pathoplexus/dev_example_data#2 for testing - see example submission in video:

Screen.Recording.2025-08-12.at.13.43.15.mov

Enable assignment of segments/subtypes using nextclade sort with the param:

classify_with_nextclade_sort: True
minimizer_index: <url_to_minimizer_index_used_by_nextclade_sort>

When this is set to true (per default) fasta headers must have the format _ (as in current set up).

Additionally instead of having a dictionary for the nextclade datasets and servers we make nucleotideSequences a list of sequences:

nextclade_dataset_name: 
    L: nextstrain/cchfv/linked/L
    M: nextstrain/cchfv/linked/M
    S: nextstrain/cchfv/linked/S
nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output
genes: [RdRp, GPC, NP]

nucleotideSequences:
  - name: L
    nextclade_dataset_name: nextstrain/cchfv/linked/L
    nextclade_dataset_tag: <optional - was previously incorrectly placed on an organism level> 
    nextclade_dataset_server: <optional overwrites nextclade_dataset_server for this seq>
    accepted_sort_matches: <optional, used for classify_with_nextclade_sort and require_nextclade_sort_match, if not given nextclade_dataset_name is used> 
    gene_prefix: <optional, prefix to add to genes produced by nextclade run, e.g. nextclade labels genes as `AV1` but we expect `EV1_AV1`, here `EV1` would be the prefix >
  - name: M
    nextclade_dataset_name: nextstrain/cchfv/linked/M
  - name: S
    nextclade_dataset_name: nextstrain/cchfv/linked/S
nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output

Note the templates now also generate the genes list from the merged config.

PR Checklist

• All necessary documentation has been adapted.
• Create a minimizer for tests using: https://github.com/loculus-project/nextclade-sort-minimizer-creator
• Any manual testing that has been done is documented (i.e. what exactly was tested?)

🚀 Preview: Add preview label to enable

[anna-parker]

closing in favor of #5402