feat(docs, website): multi path - update submission docs and templates with correct fields #5561

anna-parker · 2025-11-28T00:46:53Z

resolves #5572

Follow up PR with fastaId to fastaIds change: #5583

Screenshot

fastaIds field added to template for CCHF:

Not added for ebola or EVs:

PR Checklist

Make PR with same changes in PPX -> after docs are approved
~~[x] Add fastaIds to commonMetadata fields in config?~~ -> fastaIds field does not exist for single segmented organisms and thus should not be added here as this breaks Loculus
Ensure metadata template downloads are correct

🚀 Preview: https://multipath-docs.loculus.org

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docs/src/content/docs/reference/fasta-format.md

docs/src/content/docs/for-users/submit-sequences.md

theosanderson

Burning the midnight oil! Looks good but a few suggestions. Basically we should distinguish fastaId which is the name of a Loculus field, and "the fasta header" which is the thing it is used to link to (or maybe the "ID portion of the FASTA header" or the "FASTA entry's ID", but not the fastaId).

(I also wonder if we should call the column fastaIds since it will only be used when we expect the possibility of multiple entries?)

anna-parker · 2025-11-28T08:41:42Z

(I also wonder if we should call the column fastaIds since it will only be used when we expect the possibility of multiple entries?)

Good point! @corneliusroemer do you have any thoughts? I will otherwise make a followup PR into our "multi path branch" with that update

docs/src/content/docs/for-users/submit-sequences.md

anna-parker · 2025-11-30T17:08:50Z

@corneliusroemer and @theosanderson I tried to take both your suggestions into account - let me know what you think!

website/src/config.ts

docs/src/content/docs/for-users/submit-sequences.md

… (non-head) (#5584) 🚀 Preview: Add `preview` label to enable

theosanderson

lgtm

@theosanderson

resolves #5570 @theosanderson I am seeing a failing integration test but I think it is just flaky, let me know if you think it is an actual bug!: #5426 ### PR Checklist - [ ] All necessary documentation has been adapted. - [ ] The implemented feature is covered by appropriate, automated tests. - [ ] Any manual testing that has been done is documented (i.e. what exactly was tested?) 🚀 Preview: https://rename-fastaids.loculus.org --------- Co-authored-by: Theo Sanderson <[email protected]>

anna-parker · 2025-12-01T12:33:50Z

@corneliusroemer I will merge this now as it an overall improvement - if you have any improvements please make a PR and Im happy to review :-)

…s with correct fields (#5561) resolves #5572 Follow up PR with `fastaId` to `fastaIds` change: #5583 ### Screenshot fastaIds field added to template for CCHF: <img width="1672" height="1138" alt="image" src="https://github.com/user-attachments/assets/0dcc1be8-2f01-4205-a819-84ea8055fc5f" /> <img width="1836" height="520" alt="image" src="https://github.com/user-attachments/assets/b41678ca-17c5-41ef-a409-86288f18d124" /> Not added for ebola or EVs: <img width="1728" height="644" alt="image" src="https://github.com/user-attachments/assets/ebcfa88a-e64f-47b1-9fea-e3dfd6bd21a5" /> <img width="1836" height="520" alt="image" src="https://github.com/user-attachments/assets/a77e47ee-8f06-4a29-9eeb-68863ed3dbd0" /> ### PR Checklist - [ ] Make PR with same changes in PPX -> after docs are approved - ~[x] Add fastaIds to commonMetadata fields in config?~ -> fastaIds field does not exist for single segmented organisms and thus should not be added here as this breaks Loculus - [x] Ensure metadata template downloads are correct 🚀 Preview: https://multipath-docs.loculus.org --------- Co-authored-by: Theo Sanderson <[email protected]>

… refactor multi segment submission in backend and edit page and have prepro assign segments (#5382) resolves #4999 #4708, #4734, #5511 partially resolves #5392, #5185 (comment) includes work done in #5398 and #5402 This PR additionally fixes submission, subtype assignment and search for EVs and other multi-path organisms. ### BREAKING CHANGES When users submit to multi-segmented organisms and want to group multiple segments under one metadata entry they are now required to add an additional `fastaIds` column with a space -separated list of the `fastaId`s (fasta header IDs) of the respective sequences. If no `fastaIds` column is supplied the `submissionId` will be used instead and the backend will assume that (as in the single-segmented case) there is a one-to-one mapping of metadata `submissionId` to `fastaId`. This new submission structure was voted for in microbioinfo: https://microbial-bioinfo.slack.com/archives/CB0HYT53M/p1760961465729399 and discussed in https://app.nuclino.com/Loculus/Development/2025-10-20-Weekly-6d5fe89f-8ded-4286-b892-d215e0a498f6 (and in other meetings) Nextclade sort (uses a minimizer index for fast local alignment) or nextclade align (full sequence alignment to reference) will be used to assign segments/subtypes for all multi-segmented and multi-pathogen sequences (this is also done in ingest for grouping segments): ``` segment_classification_method: "minimizer" or "align" minimizer_url: <url_to_minimizer_index_used_by_nextclade_sort> ``` For organisms without a nextclade dataset we still allow the fasta headers to be used to determine the segment/subtype - entries must have the format `<submissionId>_<segmentName>` (as in current set up). As preprocessing now assigns segments it will return a map from the segment (or subtype) to the fastaId in the processedData, the map is called: `sequenceNameToFastaId`. This allows us to surface the segment assignment on the edit page. ### Nextclade Preprocessing pipeline config changes Instead of having a dictionary for the nextclade datasets and servers we make `nucleotideSequences` a dictionary where each item includes all information required to run nextclade. I.e. we change from: ``` 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] ``` to: ``` nextclade_sequence_and_datasets: - 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 and name are 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 > genes: [RdRp] - name: M nextclade_dataset_name: nextstrain/cchfv/linked/M genes: [GPC] - name: S nextclade_dataset_name: nextstrain/cchfv/linked/S genes: [NP] nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output segment_classification_method: <optional, default for multi segmented viruses is align - if you assign segments in ingest for grouping use the same option here as you use there e.g. "minimizer" or "align"> minimizer_url: <optional, url_to_minimizer_index_used_by_nextclade_sort> ``` ### Ingest Pipeline Config changes `minimizer_index` is changed to `minimizer_url` for consistency (can be used in ingest and preprocessing and should both be the same) ### Optional additional Config changes Limit the number of sequences the backend will accept per submission by using - should be added for multi-segmented organisms: ` submissionDataTypes: &defaultSubmissionDataTypes consensusSequences: true maxSequencesPerEntry: 1 ` ### Testing You can use pathoplexus/example_data#16 and pathoplexus/dev_example_data#2 for testing. ### PR Checklist - [x] Update values.schema.json and other READMEs - [x] add fastaId to commonMetadata (ensure it is downloaded in templates): #5561 - [x] Fix how genes are returned (will cause a config update): #5563 - [x] Improve prepro code (less duplication and more tests): #5554 - [x] ingest EVs as single segmented to ensure search works: #5511 - [x] keep tests for alignment NONE case - [x] Create a minimizer for tests using: https://github.com/loculus-project/nextclade-sort-minimizer-creator - [x] Any manual testing that has been done is documented: submission of EVs from test folder were submitted with the same fastaHeader as the submissionId -> this succeeded, additionally the submission of CCHF with a fastaID column in the metadata was tested (also in folder above), additionally revision of a segment was tested - [x] Have preprocessing send back a segment: fastaHeader mapping - ~add integration testing for full EV submission user journey~ -> will be done in a later PR - [x] improve CCHF minimizer (some segments are again not assigned) - [x] discuss if the originalData dictionary should be migrated (persistent DB has segmentName as key, now we have fastaHeader as key) -> decided against - [x] update PPX docs with new multi-segment submission format -> test PR here: pathoplexus/pathoplexus#759 - [x] update example data for demo 🚀 Preview: https://edit-page-anya.loculus.org --------- Co-authored-by: Cornelius Roemer <[email protected]> Co-authored-by: Fabian Engelniederhammer <[email protected]> Co-authored-by: Theo Sanderson <[email protected]>

anna-parker requested review from corneliusroemer, emmahodcroft and theosanderson November 28, 2025 00:46

chatgpt-codex-connector bot reviewed Nov 28, 2025

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theosanderson reviewed Nov 28, 2025

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