Helm chart config

Note

The config structure has not been finalized and may change rapidly until Loculus 1.0 is officially released (see current state and roadmap). In the meantime, this reference might also not be fully accurate or complete.

The configuration for the Helm chart is provided as a YAML file. It has the following fields:

General Settings

Field	Type	Default	Description
name	String	"Loculus"	The name of the Loculus instance
logo	Object		Configuration for the logo
logo.url	String		URL path to the logo image file
logo.width	Integer	100	Width of the logo in pixels
logo.height	Integer	100	Height of the logo in pixels
accessionPrefix	String	"LOC_"	Prefix used for accession numbers
dateFieldForGroupGraph	String, Null	null	The metadata field used to plot cumulative submissions over time on the group page (typically 'earliestReleaseDate' or another date field). Set to null to disable the chart. If the specified field does not exist for an organism, the chart will show no data for that organism.
zstdCompressionLevel	Integer	10	Zstandard compression level for sequence data. Higher means better compression ratio but higher CPU/memory usage.
pipelineVersionUpgradeCheckIntervalSeconds	Integer	10	Interval in seconds at which the backend checks for and adopts newer preprocessing pipeline versions. Pipeline version upgrades are irreversible one-time changes. The check runs on backend startup (with initial delay of min(interval, 600) seconds to avoid DB load). Higher values reduce database load but delay adoption of new pipeline versions.
environment	local, server	"server"	Deployment environment. local for development, server for production
imagePullPolicy	Always, IfNotPresent, Never	"Always"	Global image pull policy applied to all deployments. Can be overridden per-image in the images section for some images. Always: always pull the image. IfNotPresent: pull if not present locally. Never: never pull, use local image only.
podScheduling	Object	[object Object]	Pod scheduling configuration for fine-grained control over pod placement on nodes
localHost	String	"localhost"	Host string used for local development
host	String		Hostname where Loculus will be accessible
bannerMessage	String	"This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly."	Banner message (as HTML) to display at the very top of the page
bannerMessageURL	String		URL to fetch banner message HTML from - if set will be polled regularly for banner text, e.g. notice of temporary downtime, and overwrite the 'bannerMessage'-config
submissionBannerMessage	String		Banner message (as HTML) to display on submission pages
submissionBannerMessageURL	String		URL to fetch submission banner message HTML from - if set will be polled regularly for banner text on submission pages
welcomeMessageHTML	String, Null		A custom welcome message to be shown on the landing page
additionalHeadHTML	String		Additional HTML to inject into the of pages
createTestAccounts	Boolean		If true, creates the users testuser and superuser
robotsNoindexHeader	Boolean		If true, adds a noindex header to prevent search engine indexing
seqSets	Object
seqSets.enabled	Boolean		Enable/disable SeqSets. If false, seqSets.crossRef can be omitted.
seqSets.crossRef	Object, Null		Configuration for CrossRef integration. Set to null to disable CrossRef integration (you can still use SeqSets without CrossRef DOIs).
seqSets.crossRef.DOIPrefix	String		The DOI prefix for SeqSets. More information on DOI prefixes and content registration can be found here: https://www.crossref.org/services/content-registration/
seqSets.crossRef.endpoint	String		The API endpoint for CrossRef
seqSets.crossRef.databaseName	String		The database name for CrossRef
seqSets.crossRef.email	String		The email address associated with the CrossRef account
seqSets.crossRef.organization	String		The organization name for CrossRef
seqSets.crossRef.writeEnabled	Boolean	false	Enable/disable Crossref write functionality, such as generating DOIs
seqSets.fieldsToDisplay	Array		Fields to display in the SeqSets table
seqSets.graphs	Array		Graphs to display in the SeqSets statistics section
gitHubMainUrl	String	"https://github.com/loculus-project/loculus"	The link that the GitHub icon in the footer points to
gitHubIssuesUrl	String		Link to GitHub repository where users can submit issues
issuesEmail	String		Email address that users can submit issues to
sequenceFlagging.github	Object		Settings to enable sequence reporting via GitHub. If set, a button will be enabled on sequence details views to report issues with a sequence.
traefikVersion	Integer	3	Traefik major version for CRD API group. Use 2 for traefik.containo.us/v1alpha1 (Traefik v2) or 3 for traefik.io/v1alpha1 (Traefik v3).
dataUseTerms.enabled	Boolean		Whether this Loculus instance handles data use terms.
dataUseTerms.urls.open	String		A URL describing the open data use terms.
dataUseTerms.urls.restricted	String		A URL describing the restricted data use terms.
dataUseTerms.agreementHTML	String		Custom HTML for the data use terms agreement checkbox label shown in the download dialog. Can contain links and other HTML elements.
fileSharing	Object		Settings related to the file sharing feature.
fileSharing.outputFileUrlType	website, backend, s3		Whether the backend should supply file URLs as links to the website, the backend itself, or directly to the S3 server objects.
images	Object		Which docker images to use. You can specify an image spec (type) for lapis, lapisSilo, loculusSilo, website and backend.

Website Settings

Field	Type	Default	Description
website	Object		Website specific setting
website.websiteConfig	Object		Settings for the website_config.json
website.websiteConfig.enableLoginNavigationItem	Boolean	true	Whether the website should show the login button.
website.websiteConfig.enableSubmissionNavigationItem	Boolean	true	Whether the website should show "Submit" link in the top navigation bar.
website.websiteConfig.enableSubmissionPages	Boolean	true	Whether to completely disable submission related pages. Setting this to false is useful when hosting Loculus for analysis-only purposes.
website.runtimeConfig.public	Object		Settings for the public section of the runtime_config.json

User registration and authentication

Field	Type	Default	Description
auth	Object		User authentication (Keycloak settings)
auth.smtp	Object		Configuration for email sending
auth.smtp.host	String		SMTP server hostname
auth.smtp.port	Integer		SMTP server port
auth.smtp.user	String		SMTP username for authentication
auth.smtp.replyTo	String		Reply-to email address for sent emails
auth.smtp.from	String		From email address for sent emails
auth.smtp.envelopeFrom	String		Envelope from address for sent emails
auth.verifyEmail	Boolean	true	If true, requires email verification for new accounts
auth.resetPasswordAllowed	Boolean	true	If true, allows users to reset their passwords
auth.registrationAllowed	Boolean	true	If true, allows users to register new accounts in Keycloak.
auth.identityProviders.orcid.clientId	String		The client ID to use for ORCiD integration.
insecureCookies	Boolean	false	If true, allows insecure cookies.
registrationMessage	String	"You must agree to the <a href='http://main.loculus.org/terms'>terms of use</a>."	Message displayed during user registration, typically including terms of service.

Database deployments

Field	Type	Default	Description
runDevelopmentMainDatabase	Boolean	true	If true, runs a development database within the cluster.
runDevelopmentKeycloakDatabase	Boolean	true	If true, runs a development Keycloak database within the cluster.
developmentDatabasePersistence	Boolean	true	If true, makes the database on the argocd preview persistent.
runDevelopmentS3	Boolean	true	If true, runs a development MinIO S3 instance within the cluster.

For production environments, these should always be set to false. Instead, external managed databases should be used.

S3 deployments

Field	Type	Default	Description
s3.enabled	Boolean	false	Whether to enable S3. S3 is needed for the file sharing feature.
s3.gcEnabled	Boolean	false	Whether the S3 garbage collection task in the backend should delete orphan files (if true) or just output a log with orphan files (if false).
s3.gcFrequencyMinutes	Integer	1440	Frequency in minutes at which the backend runs the S3 garbage collection task.
s3.gcInitialDelayMinutes	Integer	15	How many minutes it takes before the first garbage collection task runs after the backend starts.
s3.gcOrphanRetentionPeriodMinutes	Integer	10080	Files uploaded to S3 but never attached to a sequence entry are garbage-collected after this many minutes.
s3.bucket.endpoint	String	"s3-<host value>"	The endpoint where S3 is running. Do not include a protocol prefix.
s3.bucket.region	String		The region where the bucket is located.
s3.bucket.bucket	String		The name of the bucket.

Services

Field	Type	Default	Description
disableWebsite	Boolean	false	If true, disables the frontend website deployment.
disableBackend	Boolean	false	If true, disables the backend API deployment.
disablePreprocessing	Boolean	false	If true, disables preprocessing pipelines.
disableIngest	Boolean	false	If true, disables ingestion services.
disableEnaSubmission	Boolean	false	If true, disables ENA (European Nucleotide Archive) submission service.
disableTaxonomyService	Boolean	false	If true, disables the taxonomy service deployment.
readOnlyMode	Boolean	false	If true, the instance runs in read-only mode: the backend rejects write requests (POST/PUT/DELETE/PATCH) with 503 Service Unavailable, and the website hides login/submission entry points and shows a read-only banner.

Read-only mode

Setting readOnlyMode: true at the top level of values.yaml puts the instance into a read-only state. When enabled:

• The backend rejects every mutating request (POST, PUT, PATCH, DELETE) with 503 Service Unavailable and a problem-detail body explaining that the instance is in read-only mode. GET requests continue to work.
• The website hides the Login and Submit navigation items, disables the submission pages (they return 404), skips the Keycloak redirect on pages that would otherwise enforce login (they render a read-only notice instead), and shows a banner informing users the instance is read-only.

This flag is intended for migrations, archival instances, and maintenance windows. It defaults to false.

SILO Configuration

Field	Type	Default	Description
silo	Object		Configuration for the SILO component
silo.apiThreadsForHttpConnections	Integer	16	Number of threads for HTTP connections in SILO API

Organism Configuration

Field	Type	Default	Description
organisms	Object		An object where the keys are the organism IDs and values are an Organism (type)
lineageSystemDefinitions	Object		An object where the keys are the lineage system names and values are links to lineage system definition files per pipeline version (See Lineage system definitions)

Lineage system definitions

Here’s an example of a lineageDefinitions section:

lineageSystemDefinitions:
  pangoLineage: # Lineage name to use in metadata fields
    1: https://example.org/lineage_defintions_v1.yaml # Definition per pipeline version
    2: https://example.org/lineage_defintions_v2.yaml
  myLineage:
    1: ...

Field	Type	Default	Description
lineageSystemDefinitions.<name>	Object		A map from pipeline versions to file URLs.
lineageSystemDefinitions.<name>.<pipelineVersion>	String		The URL to the lineage definition file for that lineage system and that pipeline version.

Note: Lineages should be determined by the preprocessing pipeline and not the user, set the lineage field to noInput: true to reflect this or alternatively only allow users to submit valid lineage values by adding an options list.

Hierarchical filter sources

For metadata fields whose values form a hierarchy that’s resolved at SILO import time (rather than fetched as a static file per pipeline version), set hierarchicalFilter: <URL>, where URL is the URL of the service that will create the hierarchical file for SILO. The importer collects observed values for the field, sends them to that service, and writes the returned YAML into SILO’s input directory as <MetadataName>.yaml.

Organism (type)

Each organism object has the following fields:

Field	Type	Default	Description
enabled	Boolean	true	Whether this organism is enabled.
schema	Object		Object of type organism schema
preprocessing	Array		Array of Preprocessing (type).
ingest	Object		Object of type Ingest
referenceGenomes	Array		Segment-first reference genome structure. Each segment must have a name and a list of reference genomes. Each reference contains a nucleotide sequence and optionally genes.

Organism schema (type)

Field	Type	Default	Description
organismName	String		Display name for the organism
image	String		URL to an image that will be shown on the landing page
loadSequencesAutomatically	Boolean	true	Whether sequences be loaded automatically on the sequence details page , rather than users having to press a button to do so. (For small genomes, this should probably be true.)
submissionDataTypes.consensusSequences	Boolean	true	If false, the submission form will not allow submission of consensus sequences (i.e. the sequences file must be omitted). All consensus sequence related parts on the website will be hidden.
submissionDataTypes.maxSequencesPerEntry	Integer, Null	null	Maximum number of sequences allowed per submission entry. Set to null for unlimited sequences per entry. For single-segment organisms, set to 1 to ensure only one sequence per entry.
submissionDataTypes.files.enabled	Boolean	false	If true, enable support for submitting additional files. S3 needs to be configured and categories need to be configured under categories.
submissionDataTypes.files.categories	Array		The file categories that can be submitted for this organism.
submissionDataTypes.files.categories.<fileCategory>.name	String		The name of the file category, e.g. 'raw_reads'.
submissionDataTypes.files.categories.<fileCategory>.displayName	String		The display name of the file category, e.g. 'Raw reads'.
<file>	Array		An array of output files.
<file>.[].name	String		The name of the output files array, e.g. 'annotations'.
<file>.[].displayName	String		The display name of the output files array, e.g. 'Annotations'.
<file>.[].multipleFiles	Boolean		TODO
metadata	Array		Array of Metadata fields (type) associated with the organism.
metadataAdd	Array		Array of Metadata fields (type) associated with the organism, in addtion to the fields in metadata.
metadataTemplate	Array		Array of strings. Which input fields to add to the downloadable metadata template on the submission and revision page.
nucleotideSequences	Array		Array of strings of nucleotide sequence names. Defaults to a list with just 'main'.
richFastaHeaderFields	Array		Which metadata fields to include in the fasta header when downloading sequences from the website when using the 'Display name' FASTA header style option.
linkOuts	Array		An array of external tools that can be linked to from the search page. Each linkOut has a name and URL. The URL can contain placeholders in the format [dataType] or [dataType:segment] or [dataType+rich] or [dataType:segment+rich|format] which will be replaced with the corresponding data URLs. rich means display name faster headers. You can use [metadata+col1,col2] to specify columns. Valid dataTypes are: unalignedNucleotideSequences, metadata, and alignedNucleotideSequences. You can also use {{this}} notation to URL-encode the contents of the double brackets, and you can {{nest {{these}} }}.
earliestReleaseDate	Object		Configuration object for enabling and configuring the earliestReleaseDate metadata field. For each version of an accession, the earliestReleaseDate is calculated as the earliest date of the internal release date, the dates in the configured externalFields and the value from the previous version of the accession (if there is one). This can be used when having a mix of sequences imported from other databases, as well as sequences released first in this Loculus instance, to have a field that shows the earliest release date regardless of where the sequence was first released.
earliestReleaseDate.enabled	Boolean		Whether to enable the earliestReleaseDate metadata field.
earliestReleaseDate.externalFields	Array		Field names to use when calculating the earliest release date. The fields need to be nullable strings formated with yyyy-mm-dd.
website	Object		Configuration for how the organism data is displayed on the website
website.tableColumns	Array		Columns to display in the browse table
website.defaultOrderBy	String		Default column to sort the browse table
website.defaultOrder	ascending, descending		Default order direction.
website.referenceIdentifierField	String		Must be set to use the sub-organism feature. This metadata field is used to determine which suborganism a sequence entry belongs to. N.B. the suborganism feature is incomplete and not ready for production use.
website.multiFieldSearches	Array		Define multi-field searches that allow full-text searching across multiple metadata fields of type string.

Metadata field (type)

Definition of metadata fields for sequence entries of an organism, for example the collection date and location of a sample.

Field	Type	Default	Description
name	String		Key used across app to refer to this field.
displayName	String		Name displayed to users.
type	string, int, float, number, date, boolean, authors	"string"
header	String		Grouping of fields in sequence details UI.
required	Boolean		Whether the field is required by backend.
desired	Boolean		Whether the field is a desired input field for submitters.
definition	String		Definition of input field for submitters.
guidance	String		Guidance for submitters on filling in input field.
noInput	Boolean		Whether a field with this name is expected as possible input, and so should be included in the metadata template and as a form field. (If set to true it will not be included).
notSearchable	Boolean		If true, disable search for this field.
generateIndex	Boolean		Whether the field should be indexed for search. This is only allowed for string fields and facilitates faster filters. It is recommended if the number of different values is rather small.
columnWidth	Number		The minimum column width for this field on the search table.
order	Number		Order for the column in the search table, lower first.
autocomplete	Boolean		Whether autocomplete should be offered for the field. This is only allowed for string fields and probably generateIndex should be true.
<option>	Array		An array of options for the value of this field, when it is an input field.
<option>.[].name	String		The name of the option.
enableSubstringSearch	Boolean		If true, search results will contain results that contain the given value as a substring. If false (the default), only exact matches will be returned. This only works for string fields, and you cannot also enable autocomplete.
rangeSearch	Boolean		If true, enables range search for numeric fields.
rangeOverlapSearch	Object		Config settings for enabling range overlap search.
rangeOverlapSearch.rangeName	String		The range that this field belongs to. Two fields (the upper and lower bound) need to be defined with the same range ID.
rangeOverlapSearch.rangeDisplayName	String		The display name of the range.
rangeOverlapSearch.bound	lower, upper		Whether this field is the lower or upper bound of the range.
initiallyVisible	Boolean		If true, the field is initially visible in the UI.
isSequenceFilter	Boolean		If true, this field will appear under 'Sequence Filters' on the search page instead of 'Metadata Filters'. Defaults to false.
relatesToSegment	String		Which segment this metadata field relates to. Can be set to any of the segment names defined for the organism.
percentage	Boolean		If true, the field value (expected to be between 0 and 1) is displayed as a percentage in the search filter and on the details page.
hideOnSequenceDetailsPage	Boolean		If true, hides the field on the sequence details page.
orderOnDetailsPage	Number		Determines the order on the sequence details page. Lower numbers come first. Missing values are treated as infinity, and fields will be ordered in the same order as they are defined in the config after all fields with an order value.
orderInSearchDisplay	Number		Determines the order in the search bar. Lower numbers come first. Fallback value is order (if defined) or infinity (if not defined).
hideInSearchResultsTable	Boolean		If true, hides the field in the search results table (and makes it impossible to show).
includeInDownloadsByDefault	Boolean		Whether this field should be included in metadata downloads by default.
perSegment	Boolean		Whether this is a metadata field that should exist for each segment. If so fields will be created as fieldName_A, fieldName_B in the case of an organism with segments A and B.
oneHeader	Boolean		For segmented fields, whether this field should be grouped by segment or not.
customDisplay	Object		Custom display settings for the field on the sequence details page (see here)
customDisplay.type	String
customDisplay.url	String
customDisplay.label	String		Label to display for grouped fields on the sequence details page. Overrides the field's displayName when fields are grouped via displayGroup.
onlyForReference	String		Optional. Affects the search page of the website: specify which reference the metadata field applies to, this metadata field will then only be visible if that reference is selected (in the search bar, as a table column, and in the metadata download). Must be a valid reference as defined in the reference genomes.
ontology_id	String
example	String, Number		Example value for the field.
ingest	String		Which NCBI field to map to this field.
preprocessing	Object		The values of this field will be added to the preprocessing pipeline config file and the available values depend on the chosen pipeline. For the Nextclade pipeline, please see here.
lineageSystem	String		Use this on string fields that contain lineages, if you want to enable searches that can include sublineages. The value needs to be a lineage system that is defined under the lineageSystemDefinitions key.
hierarchicalFilter	String		Use this on string fields whose values form a hierarchy resolved at SILO import time. The value should be an URL to the lineage file.
hierarchicalSearchLabel	String		CheckBox label for hierarchical search - only applies when using hierarchicalFilter.

Custom display

Use the optional customDisplay object on a metadata field to change how the value appears on the sequence details page. The object can contain type, url, html, value, linkMenuItems and displayGroup properties. The type property controls the behaviour:

• link – open the value as a hyperlink using the url where __value__ is replaced by the actual value.
• linkWithMenu – display the value as a hyperlink with a dropdown menu for multiple link options. Requires linkMenuItems array with objects containing name and url properties. The first item is used as the default/primary link that opens when clicking the value directly.
• badge – show mutation lists as coloured badges (requires value).
• htmlTemplate – replace __value__ in the provided html string and render the resulting HTML snippet.
• percentage – display numeric values as percentages.
• dataUseTerms – show the value together with a data use terms history modal.
• submittingGroup – interpret the value as JSON with group details and link to the group page.
• fileList – interpret the value as a JSON list of files and show them as download links.

When displayGroup is provided, all entries with the same group are collapsed into a single row.

Example: linkWithMenu for INSDC accessions

- name: insdcAccessionFull
  displayName: INSDC accession
  customDisplay:
    type: linkWithMenu
    linkMenuItems:
      - name: View in NCBI
        url: 'https://www.ncbi.nlm.nih.gov/nuccore/__value__'
      - name: View in ENA
        url: 'https://www.ebi.ac.uk/ena/browser/view/__value__'
      - name: View in DDBJ
        url: 'https://www.ddbj.nig.ac.jp/entry/__value__'
  header: 'INSDC'

Preprocessing (type)

Field	Type	Default	Description
version			Version of the preprocessing pipeline. Can be a single integer or an array of integers.
image	String		Docker image for the preprocessing pipeline.
dockerTag	String		Docker tag for the preprocessing pipeline.
replicas	Number		How many replicas of the prepreprocessing pipeline to run.
args	Array		Array of Strings. Arguments passed to the preprocessing pipeline.
taxonomyServiceArgs	Object		Settings to configure the taxonomy service host and port
taxonomyServiceArgs.taxonomy_service_url	String		Host and port where the taxonomy service runs
configFile	Object		Object of type ConfigFile, Fields that should be added to the preprocessing pipeline config file.

The values for args and configFile depend on the used preprocessing pipeline.

Nextclade Preprocessing Pipeline ConfigFile (type)

Field	Type	Default	Description
create_embl_file	Boolean		If prepreprocessing should generate an EMBL file for each sequence, note this requires additional metadata fields to be present (taxon_id, scientific_name, molecule_type).
alignment_requirement	ALL, ANY		Applies only to multi-segmented organisms. Determines whether ALL or ANY segments that are submitted must align. In the case ANY it must still be possible to assign the segment.
segment_classification_method	minimizer, align, diamond		Method to classify segments for multi-segmented viruses
nextclade_dataset_server	String		Server from which to download nextclade datasets.
segments	Array		Array of segment objects containing nucleotide sequences, references and their corresponding nextclade datasets.
require_nextclade_sort_match	Boolean		If true run nextclade sort and require that the highest scoring match is in the config.accepted_dataset_matches
minimizer_url	String		Minimizer used for nextclade sort (if require_nextclade_sort_match or if segments are to be assigned using nextclade sort)
backend_request_timeout_seconds	Integer		Timeout in seconds for requests to the backend server for data to process

Nextclade Preprocessing Pipeline Sequence and Dataset Objects (type)

Field	Type	Default	Description
name	String		Name of the nucleotide sequence to which this dataset applies - defaults to 'main'.
references	Array		Details of the nextclade dataset for each reference
name	String		Name of the reference to use for alignment - set name to 'singleReference' if there is only one reference.
nextclade_dataset_name	String		Name of the nextclade dataset to use to align the sequence - required if this sequence should be aligned.
nextclade_dataset_tag	String		Optional. Tag of the nextclade dataset to use to align the sequence.
nextclade_dataset_server	String		Optional. Server from which to download the nextclade dataset to use to align the sequence. If not specified, use the global nextclade_dataset_server.
accepted_dataset_matches	Array		Optional. Array of strings. The dataset names that are accepted as matches when using nextclade sort or diamond, if not specified use only accept matches with the same name or nextclade_dataset_name.
genes	Array		Array of strings. The names of the genes to be extracted from the sequence alignment results (should correspond to gene names in the nextclade dataset).
nextclade_additional_args	Array		Array of strings. Additional arguments to pass to nextclade when aligning this segment.

For more details on the Nextclade preprocessing pipeline, please see here.

Ingest (type)

Field	Type	Default	Description
image	String	"ghcr.io/loculus-project/ingest"	Docker image for the ingest pipeline
configFile	Object		Object of type ConfigFile, Fields that should be added to the ingest pipeline config file
taxon_id	Integer		NCBI taxon ID for the organism
segment_identification	Object		If multi-segmented organism, how to identify segments
muted_hashes_url	String		URL to a TSV file mapping accessions to hashes that should not trigger a revision.
grouping_override_url	String		If multi-segmented organism, URL to JSON where segment grouping overrides are defined
calculate_groups_override_json	Boolean		If multi-segmented organism, whether to calculate segment grouping overrides from assembly report data.
grouping_ignore_list_url	String		If multi-segmented organism and calculate_groups_override_json is true, URL to text file with a list of accessions which should have their GCA segment grouping ignored
metadata_filter	Object		Filter ingested sequences based on value in metadata. Filter should be a list of metadata field and value pairs.

The values for configFile depend on the used preprocessing pipeline.

Ingest ConfigFile (type)

For our ingest pipeline we require the following fields:

Field	Type	Default	Description
method	align, minimizer		Method to identify segments, uses either nextclade align or nextclade sort
nextclade_dataset_server	String
nextclade_dataset_name	String		Required if method is align
minimizer_parser	Array		Required if method is minimizer, list of the name of each '_' - separated metadata field in the minimizer index
minimizer_url	String		Required if method is minimizer
minimizer_parser_separator	String		Literal string separator used in the minimizer index dataset names (default: '_'). Avoid regex metacharacters.
backend_request_timeout_seconds	Integer		Timeout in seconds for requests to the backend server for data to process

Reference Genome (type)

Field	Type	Default	Description

NucleotideSequence (type)

Field	Type	Default	Description
name	String		Name of the reference genome
displayName	String		Display name of the reference genome used on the website (e.g., 'h1n1pdm/California/07/2009')
sequence	String		The nucleotide sequence for this segment/reference combination
insdcAccessionFull	String		INSDC accession of the sequence

Gene (type)

Field	Type	Default	Description
genes	Array		Genes for this segment/reference combination
name	String		The name of the gene
sequence	String		The amino acid or nucleotide sequence for this gene

Image spec (type)

Field	Type	Default	Description
repository	String		The repository to pull the image from. Example: ghcr.io/loculus-project/website
tag	String		The tag to pull. Examples: latest, 0.5.7. Can include a digest to absolutely pin the image (tags can move): v0.7.10.1@sha256:96e431192d6493ed71ac10bc273710df21e7c520a77bebaa7d94ff859264d36c
pullPolicy	Always, IfNotPresent, Never		The pull policy to use. Always: always pull the image. IfNotPresent: pull if not present locally. Never: never pull, use local image only.