diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
index af49e771a..9abe544e4 100644
--- a/kubernetes/loculus/values.yaml
+++ b/kubernetes/loculus/values.yaml
@@ -775,65 +775,6 @@ defaultOrganismConfig: &defaultOrganismConfig
- name: L
sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-zaire/L.fasta]]"
defaultOrganisms:
- ebola-zaire:
- <<: *defaultOrganismConfig
- preprocessing:
- - <<: *preprocessing
- configFile:
- <<: *preprocessingConfigFile
- nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/ebola/data_output
- nextclade_dataset_name: nextstrain/ebola/zaire
- ebola-sudan:
- <<: *defaultOrganismConfig
- schema:
- <<: *schema
- organismName: "Ebola Sudan"
- image: "https://www.nih.gov/sites/default/files/styles/featured_media_breakpoint-medium/public/news-events/news-releases/2023/niaid-03.jpg?itok=m4wFNGkn×tamp=1675437186"
- metadataAdd:
- - name: total_stop_codons
- type: int
- header: "Alignment states and QC metrics"
- noInput: true
- preprocessing:
- inputs: {input: nextclade.qc.stopCodons.totalStopCodons}
- - name: stop_codons
- header: "Alignment states and QC metrics"
- noInput: true
- preprocessing:
- inputs: {input: nextclade.qc.stopCodons.stopCodons}
- preprocessing:
- - <<: *preprocessing
- configFile:
- <<: *preprocessingConfigFile
- nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/ebola/data_output
- nextclade_dataset_name: nextstrain/ebola/sudan
- ingest:
- <<: *ingest
- configFile:
- taxon_id: 3052460
- referenceGenomes:
- nucleotideSequences:
- - name: "main"
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/reference.fasta]]"
- genes:
- - name: NP
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/NP.fasta]]"
- - name: VP35
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/VP35.fasta]]"
- - name: VP40
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/VP40.fasta]]"
- - name: GP
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/GP.fasta]]"
- - name: ssGP
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/ssGP.fasta]]"
- - name: sGP
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/sGP.fasta]]"
- - name: VP30
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/VP30.fasta]]"
- - name: VP24
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/VP24.fasta]]"
- - name: L
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/L.fasta]]"
mpox:
<<: *defaultOrganismConfig
schema:
@@ -901,7 +842,7 @@ defaultOrganisms:
configFile:
<<: *ingestConfigFile
taxon_id: 10244
- subsample_fraction: 0.1
+ subsample_fraction: 1.0
referenceGenomes:
nucleotideSequences:
- name: "main"
@@ -909,87 +850,10 @@ defaultOrganisms:
genes:
- name: OPG001
sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/mpox/OPG001.fasta]]"
- west-nile:
- <<: *defaultOrganismConfig
+ sars-cov-2:
schema:
- <<: *schema
- organismName: "West Nile Virus"
- image: "https://upload.wikimedia.org/wikipedia/commons/thumb/1/1e/West_Nile_Virus_Image.jpg/256px-West_Nile_Virus_Image.jpg?20200815184100"
- metadataAdd:
- - name: lineage
- header: "Lineage"
- noInput: true
- generateIndex: true
- autocomplete: true
- initiallyVisible: true
- preprocessing:
- inputs: {input: nextclade.clade}
- - name: total_stop_codons
- type: int
- header: "Alignment states and QC metrics"
- noInput: true
- preprocessing:
- inputs: {input: nextclade.qc.stopCodons.totalStopCodons}
- - name: stop_codons
- header: "Alignment states and QC metrics"
- noInput: true
- preprocessing:
- inputs: {input: nextclade.qc.stopCodons.stopCodons}
- website:
- <<: *website
- tableColumns:
- - sample_collection_date
- - ncbi_release_date
- - authors
- - author_affiliations
- - geo_loc_country
- - geo_loc_admin_1
- - length
- - lineage
- defaultOrderBy: sample_collection_date
- defaultOrder: descending
- preprocessing:
- - <<: *preprocessing
- configFile:
- <<: *preprocessingConfigFile
- nextclade_dataset_name: nextstrain/wnv/all-lineages
- nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/wnv/data_output
- genes: [capsid, prM, env, NS1, NS2A, NS2B, NS3, NS4A, 2K, NS4B, NS5]
- ingest:
- <<: *ingest
- configFile:
- taxon_id: 3048448
- referenceGenomes:
- nucleotideSequences:
- - name: main
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/reference.fasta]]"
- genes:
- - name: 2K
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/2K.fasta]]"
- - name: NS1
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS1.fasta]]"
- - name: NS2A
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS2A.fasta]]"
- - name: NS2B
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS2B.fasta]]"
- - name: NS3
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS3.fasta]]"
- - name: NS4A
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS4A.fasta]]"
- - name: NS4B
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS4B.fasta]]"
- - name: NS5
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS5.fasta]]"
- - name: capsid
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/capsid.fasta]]"
- - name: env
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/env.fasta]]"
- - name: prM
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/prM.fasta]]"
- dummy-organism:
- schema:
- image: "https://www.un.org/sites/un2.un.org/files/field/image/1583952355.1997.jpg"
- organismName: "Test Dummy Organism"
+ image: "https://raw.githubusercontent.com/corneliusroemer/demo-data/main/sars.webp"
+ organismName: "SARS-CoV-2"
metadata:
- name: date
type: date
@@ -1071,63 +935,6 @@ defaultOrganisms:
sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/ORF9b.fasta]]"
- name: "S"
sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/S.fasta]]"
- cchf:
- <<: *defaultOrganismConfig
- schema:
- <<: *schema
- organismName: "Crimean-Congo Hemorrhagic Fever Virus"
- nucleotideSequences: [L, M, S]
- image: "https://upload.wikimedia.org/wikipedia/commons/thumb/5/5e/Crimean-Congo_Hemorrhagic_Fever_%28CCHF%29_Virus_%2840689899455%29.jpg/1920px-Crimean-Congo_Hemorrhagic_Fever_%28CCHF%29_Virus_%2840689899455%29.jpg"
- website:
- <<: *website
- tableColumns:
- - sample_collection_date
- - geo_loc_country
- - geo_loc_admin_1
- - authors
- - author_affiliations
- - ncbi_release_date
- - host_name_scientific
- - length_M
- - length_S
- - length_L
- defaultOrderBy: sample_collection_date
- defaultOrder: descending
- preprocessing:
- - <<: *preprocessing
- configFile:
- <<: *preprocessingConfigFile
- log_level: DEBUG
- nextclade_dataset_name: nextstrain/cchfv/linked
- nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output
- nucleotideSequences: [L, M, S]
- genes: [RdRp, GPC, NP]
- ingest:
- <<: *ingest
- configFile:
- <<: *ingestConfigFile
- taxon_id: 3052518
- nucleotide_sequences:
- - L
- - M
- - S
- nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output
- nextclade_dataset_name: nextstrain/cchfv/linked
- referenceGenomes:
- nucleotideSequences:
- - name: L
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/reference_L.fasta]]"
- - name: M
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/reference_M.fasta]]"
- - name: S
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/reference_S.fasta]]"
- genes:
- - name: RdRp
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/RdRp.fasta]]"
- - name: GPC
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/GPC.fasta]]"
- - name: NP
- sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/NP.fasta]]"
auth:
smtp:
host: "in-v3.mailjet.com"
@@ -1192,5 +999,5 @@ enableCrossRefCredentials: true
runDevelopmentKeycloakDatabase: true
runDevelopmentMainDatabase: true
enforceHTTPS: true
-registrationTermsMessage: >
- You must agree to the terms of use.
\ No newline at end of file
+registrationTermsMessage: >-
+ You must agree to the terms of use.