openproblems-bio · sainirmayi · Oct 2, 2024 · Sep 20, 2024 · Oct 2, 2024 · Oct 2, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,7 @@
 ## Minor changes
 
 - Add the CELLxGENE immune cell atlas dataset as a common test resource (PR #907)
+- Update `dataset_id` for `tenx_visium`, `zenodo_spatial`, `zenodo_spatial_slidetags` datasets and use `mouse_brain_coronal` as a test resource in the `spatially_variable_genes` task (PR #908)
 
 # openproblems v2.0.0
 
@@ -25,7 +26,7 @@ Most relevant parts of the overall structure:
   - `openproblems_neurips2022_pbmc`: Fetch a dataset from the OpenProblems NeurIPS2022 competition
   - `openproblems_v1`: Fetch a legacy OpenProblems v1 dataset
   - `openproblems_v1_multimodal`: Fetch a legacy OpenProblems v1 multimodal dataset
-  - `tenx_vision`: Fetch a and convert 10x Visium dataset
+  - `tenx_visium`: Fetch a and convert 10x Visium dataset
   - `zenodo_spatial`: Fetch and process an Anndata file containing DBiT seq, MERFISH, seqFISH, Slide-seq v2, STARmap, and Stereo-seq data from Zenodo.
   - `zenodo_spatial_slidetags`: Download a compressed file containing gene expression matrix and spatial locations from zenodo.
 

diff --git a/src/datasets/loaders/tenx_visium/script.py b/src/datasets/loaders/tenx_visium/script.py
@@ -7,7 +7,7 @@
 par = {
   "input_expression": "https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Mouse_Brain_Rep1/CytAssist_FFPE_Mouse_Brain_Rep1_filtered_feature_bc_matrix.h5",
   "input_spatial": "https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Mouse_Brain_Rep1/CytAssist_FFPE_Mouse_Brain_Rep1_spatial.tar.gz",
-  "dataset_id": "tenx_visium/mouse_brain_coronal_section1_visium",
+  "dataset_id": "mouse_brain_coronal",
   "dataset_name": "Mouse Brain Coronal Section 1 (FFPE)",
   "dataset_url": "https://www.10xgenomics.com/datasets/mouse-brain-coronal-section-1-ffpe-2-standard",
   "dataset_summary": "Gene expression library of Mouse Brain (CytAssist FFPE) using the Mouse Whole Transcriptome Probe Set",

diff --git a/src/datasets/loaders/tenx_visium/test.py b/src/datasets/loaders/tenx_visium/test.py
@@ -4,7 +4,7 @@
 
 input_expression ="https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Mouse_Brain_Rep1/CytAssist_FFPE_Mouse_Brain_Rep1_filtered_feature_bc_matrix.h5"
 input_spatial = "https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Mouse_Brain_Rep1/CytAssist_FFPE_Mouse_Brain_Rep1_spatial.tar.gz"
-dataset_id = "10x_visium/mouse_brain_coronal_section1"
+dataset_id = "mouse_brain_coronal"
 dataset_name = "Mouse Brain Coronal Section 1 (FFPE)"
 dataset_url = "https://www.10xgenomics.com/datasets/mouse-brain-coronal-section-1-ffpe-2-standard"
 dataset_summary = "Gene expression library of Mouse Brain (CytAssist FFPE) using the Mouse Whole Transcriptome Probe Set"

diff --git a/src/datasets/resource_scripts/tenx_visium.sh b/src/datasets/resource_scripts/tenx_visium.sh
diff --git a/...ets/resource_scripts/zenodo_spatial.sh.sh → ...tasets/resource_scripts/zenodo_spatial.sh b/...ets/resource_scripts/zenodo_spatial.sh.sh → ...tasets/resource_scripts/zenodo_spatial.sh
diff --git a/src/datasets/resource_scripts/zenodo_spatial_slidetags.sh b/src/datasets/resource_scripts/zenodo_spatial_slidetags.sh
@@ -2,7 +2,7 @@
 
 cat > "/tmp/params.yaml" << 'HERE'
 param_list:
-  - id: zenodo_spatial_slidetags/human_cortex_slidetags
+  - id: zenodo_spatial_slidetags/slidetags/human_cortex
     input_data: "https://zenodo.org/records/12785822/files/slidetag_human_cortex.tar.gz?download=1"
     dataset_name: Slide-tags - Human Cortex
     dataset_url: "https://www.nature.com/articles/s41586-023-06837-4"
@@ -14,7 +14,7 @@ param_list:
     gene_filter_min_spots: 50
     remove_mitochondrial: true
 
-  - id: zenodo_spatial_slidetags/human_skin_melanoma_slidetags
+  - id: zenodo_spatial_slidetags/slidetags/human_skin_melanoma
     input_data: "https://zenodo.org/records/12785822/files/slidetag_human_skin_melanoma.tar.gz?download=1"
     dataset_name: Slide-tags - Human Skin Melanoma
     dataset_url: "https://www.nature.com/articles/s41586-023-06837-4"
@@ -26,7 +26,7 @@ param_list:
     gene_filter_min_spots: 50
     remove_mitochondrial: true
 
-  - id: zenodo_spatial_slidetags/human_tonsil_slidetags
+  - id: zenodo_spatial_slidetags/slidetags/human_tonsil
     input_data: "https://zenodo.org/records/12785822/files/slidetag_human_tonsil.tar.gz?download=1"
     dataset_name: Slide-tags - Human Tonsil
     dataset_url: "https://www.nature.com/articles/s41586-023-06837-4"
@@ -38,7 +38,7 @@ param_list:
     gene_filter_min_spots: 50
     remove_mitochondrial: true
 
-  - id: zenodo_spatial_slidetags/mouse_embryo_slidetags
+  - id: zenodo_spatial_slidetags/slidetags/mouse_embryo
     input_data: "https://zenodo.org/records/12785822/files/slidetag_mouse_embryo.tar.gz?download=1"
     dataset_name: Slide-tags - Mouse Embryo
     dataset_url: "https://www.nature.com/articles/s41586-023-06837-4"

diff --git a/...t_scripts/mouse_brain_coronal_section1.sh → ...ource_test_scripts/mouse_brain_coronal.sh b/...t_scripts/mouse_brain_coronal_section1.sh → ...ource_test_scripts/mouse_brain_coronal.sh
@@ -4,10 +4,10 @@ set -e
 
 cat > /tmp/params.yaml << 'HERE'
 param_list:
-  - id: mouse_brain_coronal_section1
+  - id: mouse_brain_coronal
     input_expression: "https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Mouse_Brain_Rep1/CytAssist_FFPE_Mouse_Brain_Rep1_filtered_feature_bc_matrix.h5"
     input_spatial: "https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/CytAssist_FFPE_Mouse_Brain_Rep1/CytAssist_FFPE_Mouse_Brain_Rep1_spatial.tar.gz"
-    dataset_name: Mouse Brain Coronal Section 1 (FFPE)
+    dataset_name: 10X Visium - Mouse Brain Coronal
     dataset_url: "https://www.10xgenomics.com/datasets/mouse-brain-coronal-section-1-ffpe-2-standard"
     dataset_summary: Gene expression library of Mouse Brain (CytAssist FFPE) using the Mouse Whole Transcriptome Probe Set
     dataset_description: "FFPE Mouse Brain tissue blocks sectioned as described in Visium CytAssist Spatial Gene Expression for FFPE - Tissue Preparation Guide Demonstrated Protocol. The H&E stained glass slide with tissue section was processed via Visium CytAssist instrument to transfer analytes to a Visium CytAssist Spatial Gene Expression slide. The probe extension and library construction steps follow the standard Visium for FFPE workflow outside of the instrument. The H&E image was acquired using Olympus VS200 Slide Scanning Microscope. Sequencing depth was 53,497 reads per spot. Sequencing configuration: 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 90bp read 2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode. Key metrics include: 2,310 spots detected under tissue; 6,736 median genes per spot; 24,862 median UMI counts per spot."

diff --git a/src/tasks/spatially_variable_genes/README.md b/src/tasks/spatially_variable_genes/README.md
@@ -83,7 +83,7 @@ flowchart LR
 A subset of the common dataset.
 
 Example file:
-`resources_test/common/mouse_brain_coronal_section1/dataset.h5ad`
+`resources_test/common//dataset.h5ad`
 
 Format:
 
@@ -142,7 +142,7 @@ Arguments:
 The dataset without spatially variable genes.
 
 Example file:
-`resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad`
+`resources_test/spatially_variable_genes//dataset.h5ad`
 
 Format:
 
@@ -177,7 +177,7 @@ Slot description:
 Anndata with true spatial variability.
 
 Example file:
-`resources_test/spatially_variable_genes/mouse_brain_coronal_section1/solution.h5ad`
+`resources_test/spatially_variable_genes//solution.h5ad`
 
 Description:
 
@@ -274,7 +274,7 @@ Arguments:
 Anndata with estimate spatial variability.
 
 Example file:
-`resources_test/spatially_variable_genes/mouse_brain_coronal_section1/output.h5ad`
+`resources_test/spatially_variable_genes//output.h5ad`
 
 Description:
 
@@ -309,7 +309,7 @@ Slot description:
 Metric score file.
 
 Example file:
-`resources_test/spatially_variable_genes/mouse_brain_coronal_section1/score.h5ad`
+`resources_test/spatially_variable_genes//score.h5ad`
 
 Format:
 

diff --git a/src/tasks/spatially_variable_genes/api/comp_control_method.yaml b/src/tasks/spatially_variable_genes/api/comp_control_method.yaml
@@ -29,6 +29,6 @@ functionality:
       path: /src/common/comp_tests/check_method_config.py
     - type: python_script
       path: /src/common/comp_tests/run_and_check_adata.py
-    - path: /resources_test/spatially_variable_genes/mouse_brain_coronal_section1
-      dest: resources_test/spatially_variable_genes/mouse_brain_coronal_section1
+    - path: /resources_test/spatially_variable_genes/mouse_brain_coronal
+      dest: resources_test/spatially_variable_genes/mouse_brain_coronal
     - path: /src/common/library.bib
diff --git a/src/tasks/spatially_variable_genes/api/comp_method.yaml b/src/tasks/spatially_variable_genes/api/comp_method.yaml
@@ -20,6 +20,6 @@ functionality:
       path: /src/common/comp_tests/check_method_config.py
     - type: python_script
       path: /src/common/comp_tests/run_and_check_adata.py
-    - path: /resources_test/spatially_variable_genes/mouse_brain_coronal_section1
-      dest: resources_test/spatially_variable_genes/mouse_brain_coronal_section1
+    - path: /resources_test/spatially_variable_genes/mouse_brain_coronal
+      dest: resources_test/spatially_variable_genes/mouse_brain_coronal
     - path: /src/common/library.bib
diff --git a/src/tasks/spatially_variable_genes/api/comp_metric.yaml b/src/tasks/spatially_variable_genes/api/comp_metric.yaml
@@ -25,7 +25,7 @@ functionality:
       path: /src/common/comp_tests/check_metric_config.py
     - type: python_script
       path: /src/common/comp_tests/run_and_check_adata.py
-    - path: /resources_test/spatially_variable_genes/mouse_brain_coronal_section1
-      dest: resources_test/spatially_variable_genes/mouse_brain_coronal_section1
+    - path: /resources_test/spatially_variable_genes/mouse_brain_coronal
+      dest: resources_test/spatially_variable_genes/mouse_brain_coronal
     - path: /src/common/library.bib
 
diff --git a/src/tasks/spatially_variable_genes/api/comp_process_dataset.yaml b/src/tasks/spatially_variable_genes/api/comp_process_dataset.yaml
@@ -23,5 +23,5 @@ functionality:
   test_resources:
     - type: python_script
       path: /src/common/comp_tests/run_and_check_adata.py
-    - path: /resources_test/common/mouse_brain_coronal_section1
-      dest: resources_test/common/mouse_brain_coronal_section1
+    - path: /resources_test/common/mouse_brain_coronal
+      dest: resources_test/common/mouse_brain_coronal
diff --git a/src/tasks/spatially_variable_genes/api/file_common_dataset.yaml b/src/tasks/spatially_variable_genes/api/file_common_dataset.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/common/mouse_brain_coronal_section1/dataset.h5ad"
+example: "resources_test/common/mouse_brain_coronal/dataset.h5ad"
 info:
   label: "Common Dataset"
   summary: A subset of the common dataset.

diff --git a/src/tasks/spatially_variable_genes/api/file_dataset.yaml b/src/tasks/spatially_variable_genes/api/file_dataset.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad"
+example: "resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad"
 info:
   label: "Dataset"
   summary: The dataset without spatially variable genes.

diff --git a/src/tasks/spatially_variable_genes/api/file_output.yaml b/src/tasks/spatially_variable_genes/api/file_output.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/spatially_variable_genes/mouse_brain_coronal_section1/output.h5ad"
+example: "resources_test/spatially_variable_genes/mouse_brain_coronal/output.h5ad"
 info:
   label: Output
   summary: "Anndata with estimate spatial variability."

diff --git a/src/tasks/spatially_variable_genes/api/file_score.yaml b/src/tasks/spatially_variable_genes/api/file_score.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/spatially_variable_genes/mouse_brain_coronal_section1/score.h5ad"
+example: "resources_test/spatially_variable_genes/mouse_brain_coronal/score.h5ad"
 info:
   label: "Score"
   summary: Metric score file.

diff --git a/src/tasks/spatially_variable_genes/api/file_simulated_dataset.yaml b/src/tasks/spatially_variable_genes/api/file_simulated_dataset.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/spatially_variable_genes/mouse_brain_coronal_section1/simulated_dataset.h5ad"
+example: "resources_test/spatially_variable_genes/mouse_brain_coronal/simulated_dataset.h5ad"
 info:
   label: "Common Dataset"
   summary: A subset of the common dataset.

diff --git a/src/tasks/spatially_variable_genes/api/file_solution.yaml b/src/tasks/spatially_variable_genes/api/file_solution.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/spatially_variable_genes/mouse_brain_coronal_section1/solution.h5ad"
+example: "resources_test/spatially_variable_genes/mouse_brain_coronal/solution.h5ad"
 info:
   label: Solution
   summary: "Anndata with true spatial variability."

diff --git a/src/tasks/spatially_variable_genes/control_methods/random_ranking/script.py b/src/tasks/spatially_variable_genes/control_methods/random_ranking/script.py
@@ -3,8 +3,8 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
-    'input_solution': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/solution.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
+    'input_solution': 'resources_test/spatially_variable_genes/mouse_brain_coronal/solution.h5ad',
     'output': 'output.h5ad'
 }
 meta = {

diff --git a/src/tasks/spatially_variable_genes/control_methods/true_ranking/script.py b/src/tasks/spatially_variable_genes/control_methods/true_ranking/script.py
@@ -2,8 +2,8 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
-    'input_solution': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/solution.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
+    'input_solution': 'resources_test/spatially_variable_genes/mouse_brain_coronal/solution.h5ad',
     'output': 'output.h5ad'
 }
 meta = {

diff --git a/src/tasks/spatially_variable_genes/methods/boostgp/script.R b/src/tasks/spatially_variable_genes/methods/boostgp/script.R
@@ -5,7 +5,7 @@ dest <- getwd()
 
 # VIASH START
 par <- list(
-    "input_data" = "resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad",
+    "input_data" = "resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad",
     "output" = "output.h5ad",
     "n_iter" = 10
 )

diff --git a/src/tasks/spatially_variable_genes/methods/gpcounts/script.py b/src/tasks/spatially_variable_genes/methods/gpcounts/script.py
@@ -10,7 +10,7 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
     'output': 'output.h5ad',
     'n_features': 120
 }

diff --git a/src/tasks/spatially_variable_genes/methods/moran_i/script.py b/src/tasks/spatially_variable_genes/methods/moran_i/script.py
@@ -6,7 +6,7 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
     'output': 'output.h5ad',
     'coord_type_moran_i': 'generic'
 

diff --git a/src/tasks/spatially_variable_genes/methods/nnsvg/script.R b/src/tasks/spatially_variable_genes/methods/nnsvg/script.R
@@ -6,7 +6,7 @@ suppressMessages(library(dplyr))
 
 # VIASH START
 par = list(
-    'input_data' = 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
+    'input_data' = 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
     'output' = 'output.h5ad'
 )
 meta = list(

diff --git a/src/tasks/spatially_variable_genes/methods/scgco/script.py b/src/tasks/spatially_variable_genes/methods/scgco/script.py
@@ -12,7 +12,7 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
     'output': 'output.h5ad'
 }
 meta = {

diff --git a/src/tasks/spatially_variable_genes/methods/sepal/script.py b/src/tasks/spatially_variable_genes/methods/sepal/script.py
@@ -3,7 +3,7 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
     'output': 'output.h5ad',
     'coord_type_sepal': 'grid',
     'max_neighs_sepal': 6,

diff --git a/src/tasks/spatially_variable_genes/methods/somde/script.py b/src/tasks/spatially_variable_genes/methods/somde/script.py
@@ -7,7 +7,7 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
     'output': 'output.h5ad'
 }
 meta = {

diff --git a/src/tasks/spatially_variable_genes/methods/spagcn/script.py b/src/tasks/spatially_variable_genes/methods/spagcn/script.py
@@ -8,7 +8,7 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
     'output': 'output.h5ad'
 }
 meta = {

diff --git a/src/tasks/spatially_variable_genes/methods/spagft/script.py b/src/tasks/spatially_variable_genes/methods/spagft/script.py
@@ -3,7 +3,7 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
     'output': 'output.h5ad'
 }
 meta = {

diff --git a/src/tasks/spatially_variable_genes/methods/spanve/script.py b/src/tasks/spatially_variable_genes/methods/spanve/script.py
@@ -3,7 +3,7 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
     'output': 'output.h5ad'
 }
 meta = {

diff --git a/src/tasks/spatially_variable_genes/methods/spark/script.R b/src/tasks/spatially_variable_genes/methods/spark/script.R
@@ -3,7 +3,7 @@ suppressMessages(library(anndata))
 
 # VIASH START
 par <- list(
-    "input_data" = "resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad",
+    "input_data" = "resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad",
     "output" = "output.h5ad"
 )
 meta <- list(

diff --git a/src/tasks/spatially_variable_genes/methods/spark_x/script.R b/src/tasks/spatially_variable_genes/methods/spark_x/script.R
@@ -3,7 +3,7 @@ suppressMessages(library(anndata))
 
 # VIASH START
 par <- list(
-    "input_data" = "resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad",
+    "input_data" = "resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad",
     "output" = "output.h5ad"
 )
 meta <- list(

diff --git a/src/tasks/spatially_variable_genes/methods/spatialde/script.py b/src/tasks/spatially_variable_genes/methods/spatialde/script.py
@@ -8,7 +8,7 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
     'output': 'output.h5ad'
 }
 meta = {

diff --git a/src/tasks/spatially_variable_genes/methods/spatialde2/script.py b/src/tasks/spatially_variable_genes/methods/spatialde2/script.py
@@ -8,7 +8,7 @@
 
 # VIASH START
 par = {
-    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/dataset.h5ad',
+    'input_data': 'resources_test/spatially_variable_genes/mouse_brain_coronal/dataset.h5ad',
     'output': 'output.h5ad'
 }
 meta = {

diff --git a/src/tasks/spatially_variable_genes/metrics/correlation/script.py b/src/tasks/spatially_variable_genes/metrics/correlation/script.py
@@ -3,8 +3,8 @@
 
 ## VIASH START
 par = {
-  'input_method': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/output.h5ad',
-  'input_solution': 'resources_test/spatially_variable_genes/mouse_brain_coronal_section1/solution.h5ad',
+  'input_method': 'resources_test/spatially_variable_genes/mouse_brain_coronal/output.h5ad',
+  'input_solution': 'resources_test/spatially_variable_genes/mouse_brain_coronal/solution.h5ad',
   'output': 'score.h5ad'
 }
 meta = {

diff --git a/src/tasks/spatially_variable_genes/process_dataset/select_reference/config.vsh.yaml b/src/tasks/spatially_variable_genes/process_dataset/select_reference/config.vsh.yaml
@@ -35,8 +35,8 @@ functionality:
     - type: python_script
       path: script.py
   test_resources:
-    - path: /resources_test/common/mouse_brain_coronal_section1
-      dest: resources_test/common/mouse_brain_coronal_section1
+    - path: /resources_test/common/mouse_brain_coronal
+      dest: resources_test/common/mouse_brain_coronal
     - type: python_script
       path: /src/common/comp_tests/run_and_check_adata.py
 platforms:

diff --git a/src/tasks/spatially_variable_genes/process_dataset/select_reference/script.py b/src/tasks/spatially_variable_genes/process_dataset/select_reference/script.py
@@ -3,7 +3,7 @@
 
 ### VIASH START
 par = {
-    "input": "resources_test/common/mouse_brain_coronal_section1/dataset.h5ad",
+    "input": "resources_test/common/mouse_brain_coronal/dataset.h5ad",
     "input_layer": "normalized",
     "output": "reference_dataset.h5ad",
     "num_features": 50,