add negative control

openproblems-bio · Aug 5, 2024 · 2f6fcdb · 2f6fcdb
1 parent 74818c8
commit 2f6fcdb
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 1 deletion.
diff --git a/src/tasks/spatially_variable_genes/resources_scripts/run_benchmark.sh b/src/tasks/spatially_variable_genes/resources_scripts/run_benchmark.sh
@@ -4,7 +4,7 @@ RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
 publish_dir="s3://openproblems-data/resources/spatially_variable_genes/results/${RUN_ID}"
 
 cat > /tmp/params.yaml << HERE
-input_states: s3://openproblems-data/resources/spatially_variable_genes/datasets/spatial_10x_xenium/**/state.yaml
+input_states: s3://openproblems-data/resources/spatially_variable_genes/datasets/**/state.yaml
 rename_keys: 'input_dataset:output_dataset,input_solution:output_solution'
 output_state: "state.yaml"
 publish_dir: "$publish_dir"

diff --git a/src/tasks/spatially_variable_genes/workflows/run_benchmark/config.vsh.yaml b/src/tasks/spatially_variable_genes/workflows/run_benchmark/config.vsh.yaml
@@ -49,6 +49,7 @@ functionality:
   dependencies:
     - name: common/check_dataset_schema
     - name: common/extract_metadata
+    - name: spatially_variable_genes/control_methods/random_ranking
     - name: spatially_variable_genes/control_methods/true_ranking
     - name: spatially_variable_genes/methods/boostgp
     - name: spatially_variable_genes/methods/gpcounts

diff --git a/src/tasks/spatially_variable_genes/workflows/run_benchmark/main.nf b/src/tasks/spatially_variable_genes/workflows/run_benchmark/main.nf
@@ -13,6 +13,7 @@ workflow run_wf {
 
   // construct list of methods
   methods = [
+    random_ranking,
     true_ranking, 
     boostgp, 
     gpcounts,