diff --git a/kubernetes/loculus/templates/loculus-preprocessing-config.yaml b/kubernetes/loculus/templates/loculus-preprocessing-config.yaml
index 41df4adfe1..cd3101d64d 100644
--- a/kubernetes/loculus/templates/loculus-preprocessing-config.yaml
+++ b/kubernetes/loculus/templates/loculus-preprocessing-config.yaml
@@ -1,12 +1,14 @@
-{{- range $key, $values := (.Values.organisms | default .Values.defaultOrganisms) }}
-{{- if $values.preprocessing.configFile }}
+{{- range $organism, $organismConfig := (.Values.organisms | default .Values.defaultOrganisms) }}
+{{- range $processingIndex, $processingConfig := $organismConfig.preprocessing }}
+{{- if $processingConfig.configFile }}
 ---
 apiVersion: v1
 kind: ConfigMap
 metadata:
-  name: loculus-preprocessing-config-{{ $key }}
+  name: loculus-preprocessing-config-{{ $organism }}-v{{ $processingConfig.version }}-{{ $processingIndex }}
 data:
   preprocessing-config.yaml: |
-    {{- $values.preprocessing.configFile | toYaml | nindent 4 -}}
+    {{- $processingConfig.configFile | toYaml | nindent 4 -}}
+{{- end }}
 {{- end }}
 {{- end }}
\ No newline at end of file
diff --git a/kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml b/kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml
index 36595e7d51..9cfde8e7ec 100644
--- a/kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml
+++ b/kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml
@@ -3,17 +3,18 @@
     "http://host.k3d.internal:8079"
     "http://loculus-backend-service:8079"
 }}
-{{- $keycloakHost := .Values.environment | eq "server" | ternary
+{{- $organismcloakHost := .Values.environment | eq "server" | ternary
     (printf "https://authentication-%s" $.Values.host)
     "http://loculus-keycloak-service:8083"
 }}
 {{- if not .Values.disablePreprocessing }}
-{{- range $key, $value := (.Values.organisms | default .Values.defaultOrganisms) }}
+{{- range $organism, $organismConfig := (.Values.organisms | default .Values.defaultOrganisms) }}
+{{- range $processingIndex, $processingConfig := $organismConfig.preprocessing }}
 ---
 apiVersion: apps/v1
 kind: Deployment
 metadata:
-  name: loculus-preprocessing-{{ $key }}
+  name: loculus-preprocessing-{{ $organism }}-v{{ $processingConfig.version }}-{{ $processingIndex }}
   annotations:
     argocd.argoproj.io/sync-options: Replace=true
     reloader.stakater.com/auto: "true"
@@ -22,43 +23,36 @@ spec:
   selector:
     matchLabels:
       app: loculus
-      component: loculus-preprocessing-{{ $key }}
+      component: loculus-preprocessing-{{ $organism }}-v{{ $processingConfig.version }}-{{ $processingIndex }}
   template:
     metadata:
       labels:
         app: loculus
-        component: loculus-preprocessing-{{ $key }}
+        component: loculus-preprocessing-{{ $organism }}-v{{ $processingConfig.version }}-{{ $processingIndex }}
     spec:
       containers:
-        - name: preprocessing-{{ $key }}
-          image: {{ $value.preprocessing.image}}:{{ $dockerTag }}
+        - name: preprocessing-{{ $organism }}
+          image: {{ $processingConfig.image}}:{{ $dockerTag }}
           imagePullPolicy: Always
           args:
-            {{- range $arg := $value.preprocessing.args }}
+            {{- range $arg := $processingConfig.args }}
             - "{{ $arg }}"
             {{- end }}
-            - "--backend-host={{ $backendHost }}/{{ $key }}"
-            - "--keycloak-host={{ $keycloakHost }}"
-            {{- if $value.preprocessing.warnings }}
-            - "--withWarnings"
-            {{- end }}
-            {{- if $value.preprocessing.errors }}
-            - "--withErrors"
-            {{- end }}
-            {{- if $value.preprocessing.randomWarnError }}
-            - "--randomWarnError"
-            {{- end }}
-      {{- if $value.preprocessing.configFile }}
+            - "--backend-host={{ $backendHost }}/{{ $organism }}"
+            - "--keycloak-host={{ $organismcloakHost }}"
+            - "--pipeline-version={{ $processingConfig.version }}"
+      {{- if $processingConfig.configFile }}
             - "--config=/etc/config/preprocessing-config.yaml"
           volumeMounts:
-            - name: loculus-preprocessing-config-volume-{{ $key }}
+            - name: preprocessing-config-volume-{{ $organism }}-v{{ $processingConfig.version }}-{{ $processingIndex }}
               mountPath: /etc/config
       volumes:
-        - name: loculus-preprocessing-config-volume-{{ $key }}
+        - name: preprocessing-config-volume-{{ $organism }}-v{{ $processingConfig.version }}-{{ $processingIndex }}
           configMap:
-            name: loculus-preprocessing-config-{{ $key }}
+            name: loculus-preprocessing-config-{{ $organism }}-v{{ $processingConfig.version }}-{{ $processingIndex }}
       {{- end }}
       imagePullSecrets:
         - name: ghcr-secret
 {{- end }}
 {{- end }}
+{{- end }}
diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
index 0fb3ca96ea..082812cdc1 100644
--- a/kubernetes/loculus/values.yaml
+++ b/kubernetes/loculus/values.yaml
@@ -62,12 +62,20 @@ defaultOrganisms:
         dateToSortBy: date
         partitionBy: pango_lineage
     preprocessing:
-      image: ghcr.io/loculus-project/preprocessing-dummy
-      args:
-        - "--watch"
-      warnings: true
-      errors: true
-      randomWarnError: true
+      - version: 1
+        image: ghcr.io/loculus-project/preprocessing-dummy
+        args:
+          - "--watch"
+          - "--withWarnings"
+          - "--withErrors"
+          - "--randomWarnError"
+      - version: 2
+        image: ghcr.io/loculus-project/preprocessing-dummy
+        args:
+          - "--watch"
+          - "--withWarnings"
+          - "--withErrors"
+          - "--randomWarnError"
     referenceGenomes:
       nucleotideSequences:
         - name: "main"
@@ -146,57 +154,108 @@ defaultOrganisms:
       silo:
         dateToSortBy: collection_date
     preprocessing:
-      image: ghcr.io/loculus-project/preprocessing-nextclade
-      args:
-        - "prepro"
-      configFile:
-        version: 1
-        log_level: DEBUG
-        nextclade_dataset_name: nextstrain/mpox/all-clades
-        nextclade_dataset_tag: 2024-01-16--20-31-02Z
-        genes:
-          OPG001: 247
-        batch_size: 100
-        processing_spec:
-          collection_date:
-            function: process_date
-            inputs:
-              date: collection_date
-              release_date: ncbi_release_date
-            required: true
-          ncbi_release_date:
-            function: parse_timestamp
-            inputs:
-              timestamp: ncbi_release_date
-          clade:
-            function: identity
-            inputs:
-              input: nextclade.clade
-          outbreak:
-            function: identity
-            inputs:
-              input: nextclade.customNodeAttributes.outbreak
-          lineage:
-            function: identity
-            inputs:
-              input: nextclade.customNodeAttributes.lineage
-          country:
-            function: identity
-            inputs:
-              input: country
-            required: true
-          author_affiliation:
-            function: identity
-            inputs:
-              input: author_affiliation
-          authors:
-            function: identity
-            inputs:
-              input: authors
-          isolate_name:
-            function: identity
-            inputs:
-              input: isolate_name
+      - version: 1
+        image: ghcr.io/loculus-project/preprocessing-nextclade
+        args:
+          - "prepro"
+        configFile:
+          log_level: DEBUG
+          nextclade_dataset_name: nextstrain/mpox/all-clades
+          nextclade_dataset_tag: 2024-01-16--20-31-02Z
+          genes:
+            OPG001: 247
+          batch_size: 100
+          processing_spec:
+            collection_date:
+              function: process_date
+              inputs:
+                date: collection_date
+                release_date: ncbi_release_date
+              required: true
+            ncbi_release_date:
+              function: parse_timestamp
+              inputs:
+                timestamp: ncbi_release_date
+            clade:
+              function: identity
+              inputs:
+                input: nextclade.clade
+            outbreak:
+              function: identity
+              inputs:
+                input: nextclade.customNodeAttributes.outbreak
+            lineage:
+              function: identity
+              inputs:
+                input: nextclade.customNodeAttributes.lineage
+            country:
+              function: identity
+              inputs:
+                input: country
+              required: true
+            author_affiliation:
+              function: identity
+              inputs:
+                input: author_affiliation
+            authors:
+              function: identity
+              inputs:
+                input: authors
+            isolate_name:
+              function: identity
+              inputs:
+                input: isolate_name
+      - version: 2
+        image: ghcr.io/loculus-project/preprocessing-nextclade
+        args:
+          - "prepro"
+        configFile:
+          log_level: DEBUG
+          nextclade_dataset_name: nextstrain/mpox/all-clades
+          nextclade_dataset_tag: 2024-01-16--20-31-02Z
+          genes:
+            OPG001: 247
+          batch_size: 100
+          processing_spec:
+            collection_date:
+              function: process_date
+              inputs:
+                date: collection_date
+                release_date: ncbi_release_date
+              required: true
+            ncbi_release_date:
+              function: parse_timestamp
+              inputs:
+                timestamp: ncbi_release_date
+            clade:
+              function: identity
+              inputs:
+                input: nextclade.clade
+            outbreak:
+              function: identity
+              inputs:
+                input: nextclade.customNodeAttributes.outbreak
+            lineage:
+              function: identity
+              inputs:
+                input: nextclade.customNodeAttributes.lineage
+            country:
+              function: identity
+              inputs:
+                input: country
+              required: true
+            author_affiliation:
+              function: identity
+              inputs:
+                input: author_affiliation
+            authors:
+              function: identity
+              inputs:
+                input: authors
+            isolate_name:
+              function: identity
+              inputs:
+                input: isolate_name
     referenceGenomes:
       nucleotideSequences:
         - name: "main"
@@ -335,173 +394,340 @@ defaultOrganisms:
       silo:
         dateToSortBy: collection_date
     preprocessing:
-      image: ghcr.io/loculus-project/preprocessing-nextclade
-      args:
-        - "prepro"
-      configFile:
-        version: 1
-        log_level: DEBUG
-        nextclade_dataset_name: nextstrain/ebola/zaire
-        nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/ebola/data_output
-        genes:
-          - NP
-          - VP35
-          - VP40
-          - GP
-          - sGP
-          - ssGP
-          - VP30
-          - VP24
-          - L
-        batch_size: 100
-        processing_spec:
-          total_snps:
-            function: identity
-            inputs:
-              input: nextclade.totalSubstitutions
-          total_inserted_nucs:
-            function: identity
-            inputs:
-              input: nextclade.totalInsertions
-          total_deleted_nucs:
-            function: identity
-            inputs:
-              input: nextclade.totalDeletions
-          total_ambiguous_nucs:
-            function: identity
-            inputs:
-              input: nextclade.totalNonACGTNs
-          total_unknown_nucs:
-            function: identity
-            inputs:
-              input: nextclade.totalMissing
-          total_frame_shifts:
-            function: identity
-            inputs:
-              input: nextclade.totalFrameShifts
-          frame_shifts:
-            function: identity
-            inputs:
-              input: nextclade.frameShifts
-          completeness:
-            function: identity
-            inputs:
-              input: nextclade.coverage
-          total_stop_codons:
-            function: identity
-            inputs:
-              input: nextclade.qc.stopCodons.totalStopCodons
-          stop_codons:
-            function: identity
-            inputs:
-              input: nextclade.qc.stopCodons.stopCodons
-          collection_date:
-            function: process_date
-            inputs:
-              date: collection_date
-              release_date: ncbi_release_date
-            required: true
-          ncbi_release_date:
-            function: parse_timestamp
-            inputs:
-              timestamp: ncbi_release_date
-          country:
-            function: identity
-            inputs:
-              input: country
-            required: true
-          author_affiliation:
-            function: identity
-            inputs:
-              input: author_affiliation
-          authors:
-            function: identity
-            inputs:
-              input: authors
-          isolate_name:
-            function: identity
-            inputs:
-              input: isolate_name
-          submitter_country:
-            function: identity
-            inputs:
-              input: submitter_country
-          division:
-            function: identity
-            inputs:
-              input: division
-          insdc_accession_base:
-            function: identity
-            inputs:
-              input: insdc_accession_base
-          insdc_version:
-            function: identity
-            inputs:
-              input: insdc_version
-          insdc_accession_full:
-            function: identity
-            inputs:
-              input: insdc_accession_full
-          bioprojects:
-            function: identity
-            inputs:
-              input: bioprojects
-          biosample_accession:
-            function: identity
-            inputs:
-              input: biosample_accession
-          ncbi_completeness:
-            function: identity
-            inputs:
-              input: ncbi_completeness
-          ncbi_host_name:
-            function: identity
-            inputs:
-              input: ncbi_host_name
-          ncbi_host_tax_id:
-            function: identity
-            inputs:
-              input: ncbi_host_tax_id
-          ncbi_is_lab_host:
-            function: identity
-            inputs:
-              input: ncbi_is_lab_host
-          ncbi_length:
-            function: identity
-            inputs:
-              input: ncbi_length
-          ncbi_protein_count:
-            function: identity
-            inputs:
-              input: ncbi_protein_count
-          ncbi_update_date:
-            function: parse_timestamp
-            inputs:
-              timestamp: ncbi_update_date
-          ncbi_sourcedb:
-            function: identity
-            inputs:
-              input: ncbi_sourcedb
-          ncbi_virus_name:
-            function: identity
-            inputs:
-              input: ncbi_virus_name
-          ncbi_virus_tax_id:
-            function: identity
-            inputs:
-              input: ncbi_virus_tax_id
-          isolate_source:
-            function: identity
-            inputs:
-              input: isolate_source
-          sra_accessions:
-            function: identity
-            inputs:
-              input: sra_accessions
-          metadata_hash:
-            function: identity
-            inputs:
-              input: metadata_hash
+      - version: 1
+        image: ghcr.io/loculus-project/preprocessing-nextclade
+        args:
+          - "prepro"
+        configFile:
+          log_level: DEBUG
+          nextclade_dataset_name: nextstrain/ebola/zaire
+          nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/ebola/data_output
+          genes:
+            - NP
+            - VP35
+            - VP40
+            - GP
+            - sGP
+            - ssGP
+            - VP30
+            - VP24
+            - L
+          batch_size: 100
+          processing_spec:
+            total_snps:
+              function: identity
+              inputs:
+                input: nextclade.totalSubstitutions
+            total_inserted_nucs:
+              function: identity
+              inputs:
+                input: nextclade.totalInsertions
+            total_deleted_nucs:
+              function: identity
+              inputs:
+                input: nextclade.totalDeletions
+            total_ambiguous_nucs:
+              function: identity
+              inputs:
+                input: nextclade.totalNonACGTNs
+            total_unknown_nucs:
+              function: identity
+              inputs:
+                input: nextclade.totalMissing
+            total_frame_shifts:
+              function: identity
+              inputs:
+                input: nextclade.totalFrameShifts
+            frame_shifts:
+              function: identity
+              inputs:
+                input: nextclade.frameShifts
+            completeness:
+              function: identity
+              inputs:
+                input: nextclade.coverage
+            total_stop_codons:
+              function: identity
+              inputs:
+                input: nextclade.qc.stopCodons.totalStopCodons
+            stop_codons:
+              function: identity
+              inputs:
+                input: nextclade.qc.stopCodons.stopCodons
+            collection_date:
+              function: process_date
+              inputs:
+                date: collection_date
+                release_date: ncbi_release_date
+              required: true
+            ncbi_release_date:
+              function: parse_timestamp
+              inputs:
+                timestamp: ncbi_release_date
+            country:
+              function: identity
+              inputs:
+                input: country
+              required: true
+            author_affiliation:
+              function: identity
+              inputs:
+                input: author_affiliation
+            authors:
+              function: identity
+              inputs:
+                input: authors
+            isolate_name:
+              function: identity
+              inputs:
+                input: isolate_name
+            submitter_country:
+              function: identity
+              inputs:
+                input: submitter_country
+            division:
+              function: identity
+              inputs:
+                input: division
+            insdc_accession_base:
+              function: identity
+              inputs:
+                input: insdc_accession_base
+            insdc_version:
+              function: identity
+              inputs:
+                input: insdc_version
+            insdc_accession_full:
+              function: identity
+              inputs:
+                input: insdc_accession_full
+            bioprojects:
+              function: identity
+              inputs:
+                input: bioprojects
+            biosample_accession:
+              function: identity
+              inputs:
+                input: biosample_accession
+            ncbi_completeness:
+              function: identity
+              inputs:
+                input: ncbi_completeness
+            ncbi_host_name:
+              function: identity
+              inputs:
+                input: ncbi_host_name
+            ncbi_host_tax_id:
+              function: identity
+              inputs:
+                input: ncbi_host_tax_id
+            ncbi_is_lab_host:
+              function: identity
+              inputs:
+                input: ncbi_is_lab_host
+            ncbi_length:
+              function: identity
+              inputs:
+                input: ncbi_length
+            ncbi_protein_count:
+              function: identity
+              inputs:
+                input: ncbi_protein_count
+            ncbi_update_date:
+              function: parse_timestamp
+              inputs:
+                timestamp: ncbi_update_date
+            ncbi_sourcedb:
+              function: identity
+              inputs:
+                input: ncbi_sourcedb
+            ncbi_virus_name:
+              function: identity
+              inputs:
+                input: ncbi_virus_name
+            ncbi_virus_tax_id:
+              function: identity
+              inputs:
+                input: ncbi_virus_tax_id
+            isolate_source:
+              function: identity
+              inputs:
+                input: isolate_source
+            sra_accessions:
+              function: identity
+              inputs:
+                input: sra_accessions
+            metadata_hash:
+              function: identity
+              inputs:
+                input: metadata_hash
+      - version: 2
+        image: ghcr.io/loculus-project/preprocessing-nextclade
+        args:
+          - "prepro"
+        configFile:
+          log_level: DEBUG
+          nextclade_dataset_name: nextstrain/ebola/zaire
+          nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/ebola/data_output
+          genes:
+            - NP
+            - VP35
+            - VP40
+            - GP
+            - sGP
+            - ssGP
+            - VP30
+            - VP24
+            - L
+          batch_size: 100
+          processing_spec:
+            total_snps:
+              function: identity
+              inputs:
+                input: nextclade.totalSubstitutions
+            total_inserted_nucs:
+              function: identity
+              inputs:
+                input: nextclade.totalInsertions
+            total_deleted_nucs:
+              function: identity
+              inputs:
+                input: nextclade.totalDeletions
+            total_ambiguous_nucs:
+              function: identity
+              inputs:
+                input: nextclade.totalNonACGTNs
+            total_unknown_nucs:
+              function: identity
+              inputs:
+                input: nextclade.totalMissing
+            total_frame_shifts:
+              function: identity
+              inputs:
+                input: nextclade.totalFrameShifts
+            frame_shifts:
+              function: identity
+              inputs:
+                input: nextclade.frameShifts
+            completeness:
+              function: identity
+              inputs:
+                input: nextclade.coverage
+            total_stop_codons:
+              function: identity
+              inputs:
+                input: nextclade.qc.stopCodons.totalStopCodons
+            stop_codons:
+              function: identity
+              inputs:
+                input: nextclade.qc.stopCodons.stopCodons
+            collection_date:
+              function: process_date
+              inputs:
+                date: collection_date
+                release_date: ncbi_release_date
+              required: true
+            ncbi_release_date:
+              function: parse_timestamp
+              inputs:
+                timestamp: ncbi_release_date
+            country:
+              function: identity
+              inputs:
+                input: country
+              required: true
+            author_affiliation:
+              function: identity
+              inputs:
+                input: author_affiliation
+            authors:
+              function: identity
+              inputs:
+                input: authors
+            isolate_name:
+              function: identity
+              inputs:
+                input: isolate_name
+            submitter_country:
+              function: identity
+              inputs:
+                input: submitter_country
+            division:
+              function: identity
+              inputs:
+                input: division
+            insdc_accession_base:
+              function: identity
+              inputs:
+                input: insdc_accession_base
+            insdc_version:
+              function: identity
+              inputs:
+                input: insdc_version
+            insdc_accession_full:
+              function: identity
+              inputs:
+                input: insdc_accession_full
+            bioprojects:
+              function: identity
+              inputs:
+                input: bioprojects
+            biosample_accession:
+              function: identity
+              inputs:
+                input: biosample_accession
+            ncbi_completeness:
+              function: identity
+              inputs:
+                input: ncbi_completeness
+            ncbi_host_name:
+              function: identity
+              inputs:
+                input: ncbi_host_name
+            ncbi_host_tax_id:
+              function: identity
+              inputs:
+                input: ncbi_host_tax_id
+            ncbi_is_lab_host:
+              function: identity
+              inputs:
+                input: ncbi_is_lab_host
+            ncbi_length:
+              function: identity
+              inputs:
+                input: ncbi_length
+            ncbi_protein_count:
+              function: identity
+              inputs:
+                input: ncbi_protein_count
+            ncbi_update_date:
+              function: parse_timestamp
+              inputs:
+                timestamp: ncbi_update_date
+            ncbi_sourcedb:
+              function: identity
+              inputs:
+                input: ncbi_sourcedb
+            ncbi_virus_name:
+              function: identity
+              inputs:
+                input: ncbi_virus_name
+            ncbi_virus_tax_id:
+              function: identity
+              inputs:
+                input: ncbi_virus_tax_id
+            isolate_source:
+              function: identity
+              inputs:
+                input: isolate_source
+            sra_accessions:
+              function: identity
+              inputs:
+                input: sra_accessions
+            metadata_hash:
+              function: identity
+              inputs:
+                input: metadata_hash
     ingest:
       args:
         - snakemake
diff --git a/preprocessing/dummy/main.py b/preprocessing/dummy/main.py
index 127cec4680..1ba5dca117 100644
--- a/preprocessing/dummy/main.py
+++ b/preprocessing/dummy/main.py
@@ -22,7 +22,7 @@
 parser.add_argument("--keycloak-password", type=str, default="dummy_preprocessing_pipeline",
                     help="Keycloak password to use for authentication")
 parser.add_argument("--keycloak-token-path", type=str, default="/realms/loculus/protocol/openid-connect/token", help="Path to Keycloak token endpoint")
-parser.add_argument("--pipelineVersion", type=int, default=1)
+parser.add_argument("--pipeline-version", type=int, default=1)
 
 args = parser.parse_args()
 backendHost = args.backend_host
@@ -34,7 +34,7 @@
 keycloakUser = args.keycloak_user
 keycloakPassword = args.keycloak_password
 keycloakTokenPath = args.keycloak_token_path
-pipelineVersion = args.pipelineVersion
+pipeline_version = args.pipeline_version
 
 
 @dataclass
@@ -62,7 +62,7 @@ def fetch_unprocessed_sequences(n: int) -> List[Sequence]:
     url = backendHost + "/extract-unprocessed-data"
     params = {
         "numberOfSequenceEntries": n,
-        "pipelineVersion": pipelineVersion
+        "pipelineVersion": pipeline_version
     }
     headers = {'Authorization': 'Bearer ' + get_jwt()}
     response = requests.post(url, data=params, headers=headers)
@@ -141,7 +141,7 @@ def process(unprocessed: List[Sequence]) -> List[Sequence]:
 def submit_processed_sequences(processed: List[Sequence]):
     json_strings = [json.dumps(dataclasses.asdict(sequence)) for sequence in processed]
     ndjson_string = '\n'.join(json_strings)
-    url = backendHost + "/submit-processed-data?pipelineVersion=" + str(pipelineVersion)
+    url = backendHost + "/submit-processed-data?pipelineVersion=" + str(pipeline_version)
     headers = {'Content-Type': 'application/x-ndjson', 'Authorization': 'Bearer ' + get_jwt()}
     response = requests.post(url, data=ndjson_string, headers=headers)
     if not response.ok:
diff --git a/preprocessing/nextclade/src/loculus_preprocessing/config.py b/preprocessing/nextclade/src/loculus_preprocessing/config.py
index 531b2d3ac9..6eb9fe1024 100644
--- a/preprocessing/nextclade/src/loculus_preprocessing/config.py
+++ b/preprocessing/nextclade/src/loculus_preprocessing/config.py
@@ -32,7 +32,7 @@ class Config:
     reference_length: int = 197209
     batch_size: int = 5
     processing_spec: dict[str, dict[str, Any]] = dataclasses.field(default_factory=dict)
-    version: int = 1
+    pipeline_version: int = 1
 
 
 def load_config_from_yaml(config_file: str, config: Config) -> Config:
diff --git a/preprocessing/nextclade/src/loculus_preprocessing/prepro.py b/preprocessing/nextclade/src/loculus_preprocessing/prepro.py
index 1af6b383d6..d3b9e347f3 100644
--- a/preprocessing/nextclade/src/loculus_preprocessing/prepro.py
+++ b/preprocessing/nextclade/src/loculus_preprocessing/prepro.py
@@ -38,7 +38,7 @@
 def fetch_unprocessed_sequences(n: int, config: Config) -> Sequence[UnprocessedEntry]:
     url = config.backend_host.rstrip("/") + "/extract-unprocessed-data"
     logging.debug(f"Fetching {n} unprocessed sequences from {url}")
-    params = {"numberOfSequenceEntries": n, "pipelineVersion": config.version}
+    params = {"numberOfSequenceEntries": n, "pipelineVersion": config.pipeline_version}
     headers = {"Authorization": "Bearer " + get_jwt(config)}
     response = requests.post(url, data=params, headers=headers, timeout=10)
     if not response.ok:
@@ -309,7 +309,7 @@ def submit_processed_sequences(processed: Sequence[ProcessedEntry], config: Conf
         "Content-Type": "application/x-ndjson",
         "Authorization": "Bearer " + get_jwt(config),
     }
-    params = {"pipelineVersion": config.version}
+    params = {"pipelineVersion": config.pipeline_version}
     response = requests.post(url, data=ndjson_string, headers=headers, params=params, timeout=10)
     if not response.ok:
         with open("failed_submission.json", "w", encoding="utf-8") as f: