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fix(docs): improve helm template values docs #3783

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fix(docs): improve helm template values docs #3783

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ef191eb
fix values docs
anna-parker Mar 3, 2025
45f0d95
fix bug
anna-parker Mar 3, 2025
2d32f53
second try
anna-parker Mar 3, 2025
e21bf91
clean up
anna-parker Mar 3, 2025
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18 changes: 12 additions & 6 deletions docs/src/content/docs/reference/helm-chart-config.mdx
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Original file line number Diff line number Diff line change
Expand Up @@ -76,19 +76,25 @@ Definition of metadata fields for sequence entries of an organism, for example t
<SchemaDocs group='preprocessing' fieldColumnClass='w-28' />

The values for `args` and `configFile` depend on the used preprocessing pipeline.
For the Nextclade preprocessing pipeline, please see

#### Nextclade Preprocessing Pipeline ConfigFile (type)
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Suggested change
#### Nextclade Preprocessing Pipeline ConfigFile (type)
#### Nextclade Preprocessing Pipeline ConfigFile

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@anna-parker anna-parker Mar 3, 2025 •
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I can remove this but now Im wondering - why do you put (type) in parenthesis for the other config components?

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the things that are types repeat in that same structure across the config (mostly). the section you added is a subsection of the properties of the type (you already used a subheading as well!) so it's not its own type IMO. That's how interpreted it! Also these type thingies are referenced in other parts of the table as "Types" (where it is just an object)


<SchemaDocs group='nextcladePipelineConfigFile' fieldColumnClass='w-28' />

For more details on the Nextclade preprocessing pipeline, please see
[here](../../for-administrators/existing-preprocessing-pipelines/#nextclade-based-pipeline).

### Ingest (type)

<SchemaDocs group='ingest' fieldColumnClass='w-28' />

The values for `configFile` depend on the used preprocessing pipeline.
For [our ingest pipeline](https://github.com/loculus-project/loculus/tree/main/ingest)
which downloads data from NCBI GenBank using NCBI Datasets, the config file needs to
contain the taxon_id of the organism and additionally, if the organism is multi-segmented,
it requires a list of segment names (nucleotide_sequences) and the nextclade_dataset that
can be used for segment identification and alignment.

#### Ingest ConfigFile (type)
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#### Ingest ConfigFile (type)
#### Ingest ConfigFile


For [our ingest pipeline](https://github.com/loculus-project/loculus/tree/main/ingest) we require the following fields:

<SchemaDocs group='ingestPipelineConfigFile' fieldColumnClass='w-28' />

### NucleotideSequence (type)

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16 changes: 8 additions & 8 deletions kubernetes/loculus/values.schema.json
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Expand Up @@ -335,19 +335,19 @@
"description": "Fields that should be added to the preprocessing pipeline config file.",
"properties": {
"alignment_requirement": {
"groups": ["ingest"],
"groups": ["nextcladePipelineConfigFile"],
"docsIncludePrefix": false,
"type": "string",
"enum": ["ALL", "ANY"],
"description": "If multi-segmented viruses should require ALL segments align or ANY segment aligns"
},
"nextclade_dataset_server": {
"groups": ["ingest"],
"groups": ["nextcladePipelineConfigFile"],
"docsIncludePrefix": false,
"type": "string"
},
"nextclade_dataset_name": {
"groups": ["ingest"],
"groups": ["nextcladePipelineConfigFile"],
"docsIncludePrefix": false,
"type": "string",
"description": "Required if sequences should be aligned"
Expand Down Expand Up @@ -391,31 +391,31 @@
"description": "If multi-segmented organism, how to identify segments",
"properties": {
"method": {
"groups": ["ingest"],
"groups": ["ingestPipelineConfigFile"],
"docsIncludePrefix": false,
"type": "string",
"enum": ["align", "minimizer"],
"description": "Method to identify segments, uses either nextclade align or nextclade sort"
},
"nextclade_dataset_server": {
"groups": ["ingest"],
"groups": ["ingestPipelineConfigFile"],
"docsIncludePrefix": false,
"type": "string"
},
"nextclade_dataset_name": {
"groups": ["ingest"],
"groups": ["ingestPipelineConfigFile"],
"docsIncludePrefix": false,
"type": "string",
"description": "Required if method is align"
},
"minimizer_parser": {
"groups": ["ingest"],
"groups": ["ingestPipelineConfigFile"],
"docsIncludePrefix": false,
"type": "array",
"description": "Required if method is minimizer, list of the name of each '_' - separated metadata field in the minimizer index"
},
"minimizer_index": {
"groups": ["ingest"],
"groups": ["ingestPipelineConfigFile"],
"docsIncludePrefix": false,
"type": "string",
"description": "Required if method is minimizer"
Expand Down
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