From 48870daf108e130aef1058edd5d09fe69e9ae02c Mon Sep 17 00:00:00 2001
From: maverbiest <maxaverbiest@gmail.com>
Date: Fri, 12 Jun 2026 15:27:30 +0200
Subject: [PATCH 1/2] Enable raw reads sharing by default

---
 kubernetes/loculus/values.yaml | 34 +++++-----------------------------
 1 file changed, 5 insertions(+), 29 deletions(-)

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
index ac55e61ca3..02eafc0a58 100644
--- a/kubernetes/loculus/values.yaml
+++ b/kubernetes/loculus/values.yaml
@@ -80,6 +80,11 @@ defaultOrganismConfig: &defaultOrganismConfig
     submissionDataTypes: &defaultSubmissionDataTypes
       consensusSequences: true
       maxSequencesPerEntry: 1
+      files:
+        enabled: true
+        categories:
+          - name: raw_reads
+            displayName: Raw reads
     loadSequencesAutomatically: true
     earliestReleaseDate:
       enabled: true
@@ -1886,35 +1891,6 @@ defaultOrganisms:
                 sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/ORF9b.fasta]]"
               - name: S
                 sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/S.fasta]]"
-  dummy-organism-with-files:
-    schema:
-      image: "/images/organisms/hmpv.jpg"
-      organismName: "Test organism (with files)"
-      submissionDataTypes:
-        consensusSequences: false
-        files:
-          enabled: true
-          categories:
-            - name: raw_reads
-              displayName: Raw reads
-      files:
-        - name: raw_reads
-          displayName: Raw reads
-      metadata: *dummyMetadata
-      website:
-        tableColumns:
-          - country
-          - division
-          - date
-        defaultOrder: descending
-        defaultOrderBy: date
-    preprocessing:
-      - version: 1
-        image: ghcr.io/loculus-project/preprocessing-dummy
-        args:
-          - "--watch"
-          - "--disableConsensusSequences"
-    referenceGenomes: []
   not-aligned-organism:
     enabled: true
     schema:

From fd2501014bc6babbec1ee66d25244be09ad1b4fd Mon Sep 17 00:00:00 2001
From: maverbiest <maxaverbiest@gmail.com>
Date: Mon, 15 Jun 2026 09:42:40 +0200
Subject: [PATCH 2/2] Add back dummy organism with files

---
 kubernetes/loculus/values.yaml | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
index 02eafc0a58..525ca21d3b 100644
--- a/kubernetes/loculus/values.yaml
+++ b/kubernetes/loculus/values.yaml
@@ -1891,6 +1891,35 @@ defaultOrganisms:
                 sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/ORF9b.fasta]]"
               - name: S
                 sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/S.fasta]]"
+  dummy-organism-with-files:
+    schema:
+      image: "/images/organisms/hmpv.jpg"
+      organismName: "Test organism (with files)"
+      submissionDataTypes:
+        consensusSequences: false
+        files:
+          enabled: true
+          categories:
+            - name: raw_reads
+              displayName: Raw reads
+      files:
+        - name: raw_reads
+          displayName: Raw reads
+      metadata: *dummyMetadata
+      website:
+        tableColumns:
+          - country
+          - division
+          - date
+        defaultOrder: descending
+        defaultOrderBy: date
+    preprocessing:
+      - version: 1
+        image: ghcr.io/loculus-project/preprocessing-dummy
+        args:
+          - "--watch"
+          - "--disableConsensusSequences"
+    referenceGenomes: []
   not-aligned-organism:
     enabled: true
     schema: