use newest values.yaml from main

loculus-project · Jun 17, 2024 · e556d24 · e556d24
1 parent 158de0e
commit e556d24
Showing 1 changed file with 17 additions and 20 deletions.
diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -63,7 +63,6 @@ defaultOrganismConfig: &defaultOrganismConfig
           function: process_date
           inputs:
             date: sample_collection_date
-            release_date: ncbi_release_date
       - name: ncbi_release_date
         displayName: NCBI release date
         type: date
@@ -141,13 +140,13 @@ defaultOrganismConfig: &defaultOrganismConfig
         header: "INSDC"
         hideOnSequenceDetailsPage: true
         noInput: true
-        per_segment: true
+        perSegment: true
       - name: insdc_version
         type: int
         header: "INSDC"
         hideOnSequenceDetailsPage: true
         noInput: true
-        per_segment: true
+        perSegment: true
       - name: insdc_accession_full
         displayName: INSDC accession
         customDisplay:
@@ -156,22 +155,22 @@ defaultOrganismConfig: &defaultOrganismConfig
         header: "INSDC"
         ingest: genbank_accession
         noInput: true
-        per_segment: true
+        perSegment: true
       - name: bioproject_accessions
         customDisplay:
           type: link
           url: "https://www.ncbi.nlm.nih.gov/bioproject/__value__"
         header: "INSDC"
         ingest: bioprojects
         noInput: true
-        per_segment: true
+        perSegment: true
       - name: biosample_accession
         customDisplay:
           type: link
           url: "https://www.ncbi.nlm.nih.gov/biosample/__value__"
         header: "INSDC"
         noInput: true
-        per_segment: true
+        perSegment: true
       - name: culture_id
         displayName: Culture ID
         header: Sample details
@@ -580,13 +579,13 @@ defaultOrganismConfig: &defaultOrganismConfig
         autocomplete: true
         header: "INSDC"
         noInput: true
-        per_segment: true
+        perSegment: true
       - name: length
         type: int
         header: "Alignment states and QC metrics"
         noInput: true
         rangeSearch: true
-        per_segment: true
+        perSegment: true
       - name: host_name_scientific
         generateIndex: true
         autocomplete: true
@@ -658,60 +657,61 @@ defaultOrganismConfig: &defaultOrganismConfig
         header: "Alignment states and QC metrics"
         noInput: true
         rangeSearch: true
+        perSegment: true
         preprocessing:
-          args: {type: int}
           inputs: {input: nextclade.totalSubstitutions}
       - name: total_inserted_nucs
         type: int
         header: "Alignment states and QC metrics"
         noInput: true
         rangeSearch: true
+        perSegment: true
         preprocessing:
-          args: {type: int}
           inputs: {input: nextclade.totalInsertions}
       - name: total_deleted_nucs
         type: int
         header: "Alignment states and QC metrics"
         noInput: true
         rangeSearch: true
+        perSegment: true
         preprocessing:
-          args: {type: int}
           inputs: {input: nextclade.totalDeletions}
       - name: total_ambiguous_nucs
         type: int
         header: "Alignment states and QC metrics"
         noInput: true
         rangeSearch: true
+        perSegment: true
         preprocessing:
-          args: {type: int}
           inputs: {input: "nextclade.totalNonACGTNs"}
       - name: total_unknown_nucs
         type: int
         header: "Alignment states and QC metrics"
         noInput: true
         rangeSearch: true
+        perSegment: true
         preprocessing:
-          args: {type: int}
           inputs: {input: nextclade.totalMissing}
       - name: total_frame_shifts
         type: int
         rangeSearch: true
         header: "Alignment states and QC metrics"
         noInput: true
+        perSegment: true
         preprocessing:
-          args: {type: int}
           inputs: {input: nextclade.totalFrameShifts}
       - name: frame_shifts
         header: "Alignment states and QC metrics"
         noInput: true
+        perSegment: true
         preprocessing:
           inputs: {input: nextclade.frameShifts}
       - name: completeness
         type: float
         header: "Alignment states and QC metrics"
         noInput: true
+        perSegment: true
         preprocessing:
-          args: {type: float}
           inputs: {input: nextclade.coverage}
     website: &website
       tableColumns:
@@ -792,7 +792,6 @@ defaultOrganisms:
           header: "Alignment states and QC metrics"
           noInput: true
           preprocessing:
-            args: {type: int}
             inputs: {input: nextclade.qc.stopCodons.totalStopCodons}
         - name: stop_codons
           header: "Alignment states and QC metrics"
@@ -867,7 +866,6 @@ defaultOrganisms:
           header: "Alignment states and QC metrics"
           noInput: true
           preprocessing:
-            args: {type: int}
             inputs: {input: nextclade.qc.stopCodons.totalStopCodons}
         - name: stop_codons
           header: "Alignment states and QC metrics"
@@ -928,7 +926,6 @@ defaultOrganisms:
           header: "Alignment states and QC metrics"
           noInput: true
           preprocessing:
-            args: {type: int}
             inputs: {input: nextclade.qc.stopCodons.totalStopCodons}
         - name: stop_codons
           header: "Alignment states and QC metrics"
@@ -1140,8 +1137,8 @@ insecureCookies: false
 bannerMessage: "This is a development environment. Data will not be persisted."
 additionalHeadHTML: '<script defer data-domain="main.loculus.org" src="https://plausible.io/js/script.js"></script>'
 images:
-  lapisSilo: "ghcr.io/genspectrum/lapis-silo:0.2.2"
-  lapis: "ghcr.io/genspectrum/lapis-v2:0.2.2"
+  lapisSilo: "ghcr.io/genspectrum/lapis-silo:0.2.3"
+  lapis: "ghcr.io/genspectrum/lapis:0.2.2"
 secrets:
   smtp-password:
     type: raw