diff --git a/src/workflows/process_datasets/config.vsh.yaml b/src/workflows/process_datasets/config.vsh.yaml
index 1fac1cd..619921d 100644
--- a/src/workflows/process_datasets/config.vsh.yaml
+++ b/src/workflows/process_datasets/config.vsh.yaml
@@ -35,14 +35,9 @@ resources:
     entrypoint: run_wf
   - path: /common/nextflow_helpers/helper.nf
 dependencies:
-  - name: common/check_dataset_schema
-    repository: openproblems_v2
+  - name: schema/verify_data_structure
+    repository: core
   - name: process_dataset/dataset_simulator
   - name: process_dataset/split_dataset
-repositories:
-  - name: openproblems_v2
-    type: github
-    repo: openproblems-bio/openproblems-v2
-    tag: main_build
 runners:
   - type: nextflow
diff --git a/src/workflows/process_datasets/main.nf b/src/workflows/process_datasets/main.nf
index 475470a..6462569 100644
--- a/src/workflows/process_datasets/main.nf
+++ b/src/workflows/process_datasets/main.nf
@@ -14,7 +14,7 @@ workflow run_wf {
   main:
   output_ch = input_ch
 
-    | check_dataset_schema.run(
+    | verify_data_structure.run(
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "input")
         def schemaYaml = tempFile("schema.yaml")
diff --git a/src/workflows/process_datasets/run_test.sh b/src/workflows/process_datasets/run_test.sh
deleted file mode 100644
index 1fae69c..0000000
--- a/src/workflows/process_datasets/run_test.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-
-RAW_DATA=resources_test/common
-DATASET_DIR=resources_test/spatial_decomposition
-echo "Running process_dataset"
-nextflow run . \
-    -main-script target/nextflow/workflows/process_datasets/main.nf \
-    -profile docker \
-    -entry auto \
-    -c common/nextflow_helpers/labels_ci.config \
-    --input_states "$RAW_DATA/**/state.yaml" \
-    --rename_keys 'input:output_dataset' \
-    --settings '{"output_spatial_masked": "$id/spatial_masked.h5ad", "output_single_cell": "$id/single_cell_ref.h5ad", "output_solution": "$id/solution.h5ad", "alpha": 1.0, "simulated_data": "$id/simulated_dataset.h5ad"}' \
-    --publish_dir "$DATASET_DIR" \
-    --output_state '$id/state.yaml'
\ No newline at end of file
diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
index cfa3a32..5eb01e8 100644
--- a/src/workflows/run_benchmark/config.vsh.yaml
+++ b/src/workflows/run_benchmark/config.vsh.yaml
@@ -48,10 +48,8 @@ resources:
     path: main.nf
     entrypoint: run_wf
 dependencies:
-  - name: common/check_dataset_schema
-    repository: openproblems_v2
-  - name: common/extract_metadata
-    repository: openproblems_v2
+  - name: h5ad/extract_uns_metadata
+    repository: core
   - name: control_methods/random_proportions
   - name: control_methods/true_proportions
   - name: methods/cell2location
diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf
index ca2216c..5a6437c 100644
--- a/src/workflows/run_benchmark/main.nf
+++ b/src/workflows/run_benchmark/main.nf
@@ -42,7 +42,7 @@ workflow run_wf {
     }
     
     // extract the dataset metadata
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       fromState: [input: "input_solution"],
       toState: { id, output, state ->
         state + [
@@ -150,7 +150,7 @@ workflow run_wf {
   output_ch = score_ch
 
     // extract the scores
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       key: "extract_scores",
       fromState: [input: "metric_output"],
       toState: { id, output, state ->
diff --git a/src/workflows/run_benchmark/run_test.sh b/src/workflows/run_benchmark/run_test.sh
deleted file mode 100644
index 55a2d96..0000000
--- a/src/workflows/run_benchmark/run_test.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/bin/bash
-
-DATASETS_DIR="resources/pancreas"
-OUTPUT_DIR="output/temp"
-if [ ! -d "$OUTPUT_DIR" ]; then
-  mkdir -p "$OUTPUT_DIR"
-fi
-echo "Running the benchmark"
-nextflow run . \
-  -main-script target/nextflow/workflows/run_benchmark/main.nf \
-  -profile docker \
-  -resume \
-  -entry auto \
-  -c common/nextflow_helpers/labels_ci.config \
-  --input_states "$DATASETS_DIR/state.yaml" \
-  --rename_keys 'input_single_cell:output_single_cell;input_spatial_masked:output_spatial_masked;input_solution:output_solution' \
-  --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \
-  --publish_dir "$OUTPUT_DIR" \
-  --output_state "state.yaml"
\ No newline at end of file